Body: <p>Im trying to run ProtDeform on ubuntu 20.04
  <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125161/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125161/</a>
  I need scoring function :/ to my project</p>
  <p>But error occurs:</p>
  <pre><code>(base) marcin@marcin-B550-AORUS-ELITE-AX-V2:~/ProtDeformV1.0$ ./install 
  rm: cannot remove 'ProtDeform': No such file or directory
  Compiling...
  gcc -c  -g Matras.c Amino.c Vector.c GotohDPdis.c DiffStr.c BetaTopo.c RegressL.c Jacobi3.c SecStrEle.c ScoreENV.c ScoreDIS.c ScoreSSE.c BuildUpL.c DiheDis.c RMS.c OutAln.c StrLibL.c OutLibL.c LlistIO.c CalZsc.c LlistAlign.c MergeSort.c PairAli.c IO.c
  Matras.c:77:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
     77 | main(argc,argv)
        | ^~~~
  Matras.c: In function ‘main’:
  Matras.c:126:3: warning: implicit declaration of function ‘Set_AAnum’ [-Wimplicit-function-declaration]
    126 |   Set_AAnum();
        |   ^~~~~~~~~
  Matras.c:390:27: warning: zero-length gnu_printf format string [-Wformat-zero-length]
    390 |         sprintf(envscfile,&quot;&quot;);
        |                           ^~
  Matras.c:431:23: warning: zero-length gnu_printf format string [-Wformat-zero-length]
    431 |   sprintf(PAR.COMMAND,&quot;&quot;);
        |                       ^~
  Matras.c:436:29: warning: implicit declaration of function ‘Get_Date_String’; did you mean ‘Get_Time_String’? [-Wimplicit-function-declaration]
    436 |   printf(&quot;#&lt;DATE&gt; \&quot;%s\&quot;\n&quot;,Get_Date_String());
        |                             ^~~~~~~~~~~~~~~
        |                             Get_Time_String
  Matras.c:436:22: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
    436 |   printf(&quot;#&lt;DATE&gt; \&quot;%s\&quot;\n&quot;,Get_Date_String());
        |                     ~^      ~~~~~~~~~~~~~~~~~
        |                      |      |
        |                      char * int
        |                     %d
  Matras.c:442:10: warning: too many arguments for format [-Wformat-extra-args]
    442 |   printf(&quot;# QueFile \&quot;%s\&quot; LibFile \&quot;%s\&quot;\n&quot;,MODE,QueFile,LibFile);
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Matras.c:498:4: warning: implicit declaration of function ‘Pairwise_3D_Alignment’ [-Wimplicit-function-declaration]
    498 |    Pairwise_3D_Alignment(&amp;proA,&amp;proB,&amp;DmapA,&amp;DmapB,&amp;AHead,&amp;SHead,inalifile,inssefile);
        |    ^~~~~~~~~~~~~~~~~~~~~
  Matras.c:502:4: warning: implicit declaration of function ‘mainPD’; did you mean ‘main’? [-Wimplicit-function-declaration]
    502 |    mainPD(&amp;proA, &amp;proB, AHead.next, inalifile ); /* JR ProtDeform */
        |    ^~~~~~
        |    main
  Matras.c:529:5: warning: implicit declaration of function ‘Output_Path_Horizontal_ClustalW’; did you mean ‘Output_Path_Horizontal_HTMLcolor’? [-Wimplicit-function-declaration]
    529 |     Output_Path_Horizontal_ClustalW(&amp;proA,&amp;proB,an,outclwfile);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        |     Output_Path_Horizontal_HTMLcolor
  Matras.c:726:6: warning: implicit declaration of function ‘Cal_Raw_MeanSD_Llist’; did you mean ‘Cal_Raw_Zscore_Llist’? [-Wimplicit-function-declaration]
    726 |      Cal_Raw_MeanSD_Llist(&amp;ALibHead,&amp;Mean,&amp;SD);
        |      ^~~~~~~~~~~~~~~~~~~~
        |      Cal_Raw_Zscore_Llist
  Matras.c:512:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
    512 |     sprintf(OutHead,&quot;%s%d&quot;,OheadStr,an-&gt;num);
        |                          ^
  Matras.c:512:5: note: ‘sprintf’ output between 2 and 139 bytes into a destination of size 128
    512 |     sprintf(OutHead,&quot;%s%d&quot;,OheadStr,an-&gt;num);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Matras.c:587:43: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 113 and 240 [-Wformat-overflow=]
    587 |      { sprintf(command,&quot;perl %s/rotSTR.pl %s.mat %s -nc A -S B &gt; %s.pdb&quot;,
        |                                           ^~
    588 |              BASE_DIR,OutHead,proAfile,OutHead);
        |                       ~~~~~~~              
  Matras.c:587:8: note: ‘sprintf’ output between 40 and 484 bytes into a destination of size 256
    587 |      { sprintf(command,&quot;perl %s/rotSTR.pl %s.mat %s -nc A -S B &gt; %s.pdb&quot;,
        |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    588 |              BASE_DIR,OutHead,proAfile,OutHead);
        |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Matras.c:590:62: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 33 and 223 [-Wformat-overflow=]
    590 |        sprintf(command,&quot;perl %s/rotSTR.pl - %s -nc B -S B &gt;&gt; %s.pdb&quot;,BASE_DIR,proBfile,OutHead);
        |                                                              ^~                        ~~~~~~~
  Matras.c:590:8: note: ‘sprintf’ output between 38 and 355 bytes into a destination of size 256
    590 |        sprintf(command,&quot;perl %s/rotSTR.pl - %s -nc B -S B &gt;&gt; %s.pdb&quot;,BASE_DIR,proBfile,OutHead);
        |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Matras.c:594:43: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 113 and 240 [-Wformat-overflow=]
    594 |      { sprintf(command,&quot;perl %s/rotSTR.pl %s.mat %s -nc A -S P -ch %c -H W &gt; %s.pdb&quot;,
        |                                           ^~
    595 |            BASE_DIR,OutHead,proAfile,proA.chain,OutHead);
        |                     ~~~~~~~                
  Matras.c:594:8: note: ‘sprintf’ output between 51 and 495 bytes into a destination of size 256
    594 |      { sprintf(command,&quot;perl %s/rotSTR.pl %s.mat %s -nc A -S P -ch %c -H W &gt; %s.pdb&quot;,
        |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    595 |            BASE_DIR,OutHead,proAfile,proA.chain,OutHead);
        |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Matras.c:597:73: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 23 and 213 [-Wformat-overflow=]
    597 |       sprintf(command,&quot;perl %s/rotSTR.pl - %s -nc B -S P -ch %c -H W&gt;&gt; %s.pdb&quot;,
        |                                                                        ^~
  
    598 |         BASE_DIR,proBfile,proB.chain,OutHead);
        |                                      ~~~~~~~                            
  
  Matras.c:597:8: note: ‘sprintf’ output between 48 and 365 bytes into a destination of size 256
    597 |        sprintf(command,&quot;perl %s/rotSTR.pl - %s -nc B -S P -ch %c -H W&gt;&gt; %s.pdb&quot;,
        |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    598 |          BASE_DIR,proBfile,proB.chain,OutHead);
        |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Amino.c: In function ‘Amino_Name’:
  Amino.c:104:11: warning: implicit declaration of function ‘strncmp’ [-Wimplicit-function-declaration]
    104 |       if (strncmp(t,&quot;ALA&quot;,3)==0)  r = 'A';
        |           ^~~~~~~
  Amino.c:104:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    104 |       if (strncmp(t,&quot;ALA&quot;,3)==0)  r = 'A';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:105:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    105 |  else if (strncmp(t,&quot;GLU&quot;,3)==0)  r = 'E';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:106:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    106 |  else if (strncmp(t,&quot;GLN&quot;,3)==0)  r = 'Q';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:107:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    107 |  else if (strncmp(t,&quot;ASP&quot;,3)==0)  r = 'D';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:108:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    108 |  else if (strncmp(t,&quot;ASN&quot;,3)==0)  r = 'N';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:109:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    109 |  else if (strncmp(t,&quot;LEU&quot;,3)==0)  r = 'L';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:110:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    110 |  else if (strncmp(t,&quot;GLY&quot;,3)==0)  r = 'G';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:111:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    111 |  else if (strncmp(t,&quot;LYS&quot;,3)==0)  r = 'K';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:112:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    112 |  else if (strncmp(t,&quot;SER&quot;,3)==0)  r = 'S';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:113:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    113 |  else if (strncmp(t,&quot;VAL&quot;,3)==0)  r = 'V';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:114:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    114 |  else if (strncmp(t,&quot;ARG&quot;,3)==0)  r = 'R';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:115:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    115 |  else if (strncmp(t,&quot;THR&quot;,3)==0)  r = 'T';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:116:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    116 |  else if (strncmp(t,&quot;PRO&quot;,3)==0)  r = 'P';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:117:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    117 |  else if (strncmp(t,&quot;ILE&quot;,3)==0)  r = 'I';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:118:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    118 |  else if (strncmp(t,&quot;MET&quot;,3)==0)  r = 'M';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:119:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    119 |  else if (strncmp(t,&quot;PHE&quot;,3)==0)  r = 'F';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:120:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    120 |  else if (strncmp(t,&quot;TYR&quot;,3)==0)  r = 'Y';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:121:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    121 |  else if (strncmp(t,&quot;CYS&quot;,3)==0)  r = 'C';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:122:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    122 |  else if (strncmp(t,&quot;TRP&quot;,3)==0)  r = 'W';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:123:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    123 |  else if (strncmp(t,&quot;HIS&quot;,3)==0)  r = 'H';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:124:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    124 |  else if (strncmp(t,&quot;UNK&quot;,3)==0)  r = 'u';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:125:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    125 |  else if (strncmp(t,&quot;ACE&quot;,3)==0)  r = 'a';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  Amino.c:126:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    126 |  else if (strncmp(t,&quot;FOR&quot;,3)==0)  r = 'f';
        |                           ^
  &lt;built-in&gt;: note: built-in ‘strncmp’ declared here
  GotohDPdis.c: In function ‘GotohDP_Dscore_Iterative’:
  GotohDPdis.c:202:3: warning: implicit declaration of function ‘ScoreDistanceSPair’; did you mean ‘ScoreDistanceS’? [-Wimplicit-function-declaration]
    202 |   ScoreDistanceSPair(proA,proB,an,DmapA,DmapB);
        |   ^~~~~~~~~~~~~~~~~~
        |   ScoreDistanceS
  GotohDPdis.c: In function ‘GotohDP_Dscore’:
  GotohDPdis.c:223:33: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
    223 |   { printf(&quot;#ERROR:PRE.MaxNali %s is less than Nali %d\n&quot;,PRE.MaxNali,an-&gt;Nali);
        |                                ~^                         ~~~~~~~~~~~
        |                                 |                            |
        |                                 char *                       int
        |                                %d
  DiffStr.c: In function ‘Number_Sec’:
  DiffStr.c:202:5: warning: type of ‘sym’ defaults to ‘int’ [-Wimplicit-int]
    202 | int Number_Sec(sym,Nstr)
        |     ^~~~~~~~~~
  SecStrEle.c: In function ‘Output_SSE_PDB’:
  SecStrEle.c:355:13: warning: too many arguments for format [-Wformat-extra-args]
    355 |  fprintf(fp,&quot;REMARK tFactor : 0 for Cend of SSE, 200 for  helix, 100 for sheet\n&quot;,pr-&gt;pname);
        |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ScoreENV.c: In function ‘Number_Sec’:
  ScoreENV.c:313:5: warning: type of ‘sym’ defaults to ‘int’ [-Wimplicit-int]
    313 | int Number_Sec(sym,Nstr)
        |     ^~~~~~~~~~
  ScoreENV.c: In function ‘Read_Env_Score’:
  ScoreENV.c:264:22: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
    264 |  sprintf(Fname,&quot;%s/%s&quot;,SCORE_DIR,fname);
        |                      ^
  ScoreENV.c:264:2: note: ‘sprintf’ output 2 or more bytes (assuming 129) into a destination of size 128
    264 |  sprintf(Fname,&quot;%s/%s&quot;,SCORE_DIR,fname);
        |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  BuildUpL.c: In function ‘Build_Up_LL’:
  BuildUpL.c:256:2: warning: implicit declaration of function ‘Merge_Sort_Double_Linked_List’ [-Wimplicit-function-declaration]
    256 |  Merge_Sort_Double_Linked_List(head,'R');
        |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  BuildUpL.c: In function ‘Read_SSE_Alignment’:
  BuildUpL.c:677:4: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
    677 |    Get_Part_Of_Line(num1,word1,1,strlen(word1));
        |    ^~~~~~~~~~~~~~~~
  OutAln.c: In function ‘Write_Rasmol_Color_Alignment’:
  OutAln.c:564:34: warning: implicit declaration of function ‘Get_Date_String’ [-Wimplicit-function-declaration]
    564 |  fprintf(fp,&quot;# DATE      '%s'\n&quot;,Get_Date_String());
        |                                  ^~~~~~~~~~~~~~~
  OutAln.c:564:28: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
    564 |  fprintf(fp,&quot;# DATE      '%s'\n&quot;,Get_Date_String());
        |                           ~^     ~~~~~~~~~~~~~~~~~
        |                            |     |
        |                            |     int
        |                            char *
        |                           %d
  OutAln.c: In function ‘Write_Rasmol_Color_Alignment_Each_Protein’:
  OutAln.c:715:27: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
    715 |  fprintf(fp,&quot;# DATE      %s\n&quot;,Get_Date_String());
        |                          ~^    ~~~~~~~~~~~~~~~~~
        |                           |    |
        |                           |    int
        |                           char *
        |                          %d
  OutAln.c:731:10: warning: implicit declaration of function ‘Ncompare’ [-Wimplicit-function-declaration]
    731 |  Ncomp = Ncompare(a);
        |          ^~~~~~~~
  OutAln.c: In function ‘Write_Molscript_Alignment_Each_Protein’:
  OutAln.c:880:27: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
    880 |  fprintf(fp,&quot;! DATE      %s\n&quot;,Get_Date_String());
        |                          ~^    ~~~~~~~~~~~~~~~~~
        |                           |    |
        |                           |    int
        |                           char *
        |                          %d
  OutAln.c:905:35: warning: implicit declaration of function ‘Remove_Space’ [-Wimplicit-function-declaration]
    905 |        if (OutProteinType == 'A') Remove_Space(rsta,pA-&gt;Rnum[a-&gt;nalA[i]]);
        |                                   ^~~~~~~~~~~~
  OutAln.c: In function ‘Find_nal’:
  OutAln.c:962:5: warning: type of ‘q’ defaults to ‘int’ [-Wimplicit-int]
    962 | int Find_nal(q,Nali,nalA)
        |     ^~~~~~~~
  OutAln.c: In function ‘Output_Alignment_Information’:
  OutAln.c:1058:2: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
   1058 |  Get_Part_Of_Line(ln,pA-&gt;compnd,0,40);
        |  ^~~~~~~~~~~~~~~~
  StrLibL.c: In function ‘Read_Library_List’:
  StrLibL.c:75:5: warning: implicit declaration of function ‘Get_First_Field’ [-Wimplicit-function-declaration]
     75 |     Get_First_Field(name,tax,buffer);
        |     ^~~~~~~~~~~~~~~
  StrLibL.c: In function ‘Check_Library_List’:
  StrLibL.c:113:3: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
    113 |   Get_Part_Of_Line(dir,bn-&gt;Name,1,2);
        |   ^~~~~~~~~~~~~~~~
  OutLibL.c: In function ‘Output_Library_ClustalW’:
  OutLibL.c:234:4: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
    234 |    Get_Part_Of_Line(ln,bn-&gt;sim-&gt;Name,0,16);
        |    ^~~~~~~~~~~~~~~~
  LlistIO.c: In function ‘Read_BSSP_File_LinearList’:
  LlistIO.c:161:2: warning: implicit declaration of function ‘Set_SSE’ [-Wimplicit-function-declaration]
    161 |  Set_SSE(pr);
        |  ^~~~~~~
  LlistIO.c:162:2: warning: implicit declaration of function ‘Set_Dis_bwn_SSE’ [-Wimplicit-function-declaration]
    162 |  Set_Dis_bwn_SSE(pr,'C');
        |  ^~~~~~~~~~~~~~~
  LlistIO.c: In function ‘Translate_BSSP_File_LinearList’:
  LlistIO.c:218:51: warning: implicit declaration of function ‘tolower’ [-Wimplicit-function-declaration]
    218 |             if (X-&gt;line[75]=='C') pr-&gt;Seq[Rnum] = tolower(pr-&gt;Seq[Rnum]);  /* for CIS conf */
        |                                                   ^~~~~~~
  PairAli.c: In function ‘Pairwise_3D_Alignment’:
  PairAli.c:188:3: warning: implicit declaration of function ‘Set_Value_AlignNode’; did you mean ‘Tail_Value_AlignNode’? [-Wimplicit-function-declaration]
    188 |   Set_Value_AlignNode(Ahead,'S');    /* JR  It was  D */
        |   ^~~~~~~~~~~~~~~~~~~
        |   Tail_Value_AlignNode
  PairAli.c:189:3: warning: implicit declaration of function ‘Merge_Sort_Double_Linked_List’ [-Wimplicit-function-declaration]
    189 |   Merge_Sort_Double_Linked_List(Ahead,'R');
        |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  IO.c: In function ‘Read_BSSP_File’:
  IO.c:705:3: warning: implicit declaration of function ‘Set_SSE’ [-Wimplicit-function-declaration]
    705 |   Set_SSE(pr);
        |   ^~~~~~~
  IO.c:706:3: warning: implicit declaration of function ‘Set_Dis_bwn_SSE’ [-Wimplicit-function-declaration]
    706 |   Set_Dis_bwn_SSE(pr,'C');
        |   ^~~~~~~~~~~~~~~
  IO.c: In function ‘Read_Sequence’:
  IO.c:886:13: warning: implicit declaration of function ‘isalpha’ [-Wimplicit-function-declaration]
    886 |    else if (isalpha(sym)!=0)
        |             ^~~~~~~
  IO.c: In function ‘Read_Matras_Environment_File’:
  IO.c:87:23: warning: ‘%s’ directive writing up to 63 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
     87 |   sprintf(Matfile,&quot;%s/%s&quot;,homedir,matfile);
        |                       ^~          ~~~~~~~
  IO.c:87:3: note: ‘sprintf’ output between 2 and 192 bytes into a destination of size 128
     87 |   sprintf(Matfile,&quot;%s/%s&quot;,homedir,matfile);
        |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  IO.c: In function ‘Read_PDB_File’:
  IO.c:378:20: warning: ‘%s’ directive writing up to 3 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
    378 |  sprintf(Fname,&quot;%s/%s/%s&quot;,PDB_DIR,dir,fname);
        |                    ^~             ~~~
  IO.c:378:2: note: ‘sprintf’ output 3 or more bytes (assuming 133) into a destination of size 128
    378 |  sprintf(Fname,&quot;%s/%s/%s&quot;,PDB_DIR,dir,fname);
        |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  g++ -c  -g vector.cpp TransSeq.cpp Geometry.cpp WriteDeformPDB.cpp Evaluation.cpp  -w
  Geometry.cpp:30:31: error: ‘&lt;unnamed enum&gt; GEOMETRY’, declared using unnamed type, is used but never defined [-fpermissive]
     30 | extern enum { RIGID, AFFINE } GEOMETRY;
        |                               ^~~~~~~~
  WriteDeformPDB.cpp:16:31: error: ‘&lt;unnamed enum&gt; GEOMETRY’, declared using unnamed type, is used but never defined [-fpermissive]
     16 | extern enum { RIGID, AFFINE } GEOMETRY;
        |                               ^~~~~~~~
  make: *** [Makefile:125: ../ProtDeform] Error 1
  </code></pre>
  <p>I've contacted the program developers about this, but am still waiting for answer from them.</p>
  <p>Can you help?</p>
  <p>EDIT1:
  ox
  I've checked</p>
  <p>Ubuntu 16.04 on virtualbox</p>
  <p>Ubuntu 20.04 with i7</p>
  <p>Ubuntu 20.04 with Ryzen 9</p>
  <p>same error...</p>
  <p>EDIT 2:</p>
  <pre><code>I have found hidden file .matras:
  ###############################
  ### MATRAS ENVIRONMENT FILE ###
  ###############################
  
  BASE_DIR .
  SCORE_DIR  data_sc/ROM-04JAN29
  TMP_DIR    .
  BSSP_DIR  /DB/BSSP
  PDB_DIR   /DB/PDB
  </code></pre>
  <p>I'm checking to see if it simply requires PDB</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-13T01:54:33.760Z
Comments.Text: What is ProtDeform? Why are you trying to use it? Can you give any additional context around your problem that would help in finding a solution?
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-13T09:57:27.180Z
Comments.Text: @gringer I add some information. Yes, still waiting for answer :/
Comments.UserDisplayName: MTG
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-15T17:24:01.710Z
Comments.Text: The tool is more than 10 years old, without documentation for compilation and without any documentation towards software versions. The paper has a single citation, indication it never has been adopted by the community. Hence, find something else that actually works. Not what you want to hear, I know.
Comments.UserDisplayName: ATpoint
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-15T21:27:15.917Z
Comments.Text: is this webserver giving any result with your input https://bioinfo.uib.es/~recerca/ProtDeform/
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-15T21:29:40.973Z
Comments.Text: are you trying to run or install the software ??
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-16T07:36:50.373Z
Comments.Text: @pippo1980 install to run :)
Comments.UserDisplayName: MTG
Tags: <proteins><protein-structure><bash><perl>
Title: Old program make error ProtDeform
ThreadText: # Old program make error ProtDeform
  
  (Asked by: username_0 on 2023-09-12)
  
  Im trying to run ProtDeform on ubuntu 20.04
  <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125161/>
  I need scoring function :/ to my project
  
  But error occurs:
  
  ```
  (base) marcin@marcin-B550-AORUS-ELITE-AX-V2:~/ProtDeformV1.0$ ./install 
  rm: cannot remove 'ProtDeform': No such file or directory
  Compiling...
  gcc -c  -g Matras.c Amino.c Vector.c GotohDPdis.c DiffStr.c BetaTopo.c RegressL.c Jacobi3.c SecStrEle.c ScoreENV.c ScoreDIS.c ScoreSSE.c BuildUpL.c DiheDis.c RMS.c OutAln.c StrLibL.c OutLibL.c LlistIO.c CalZsc.c LlistAlign.c MergeSort.c PairAli.c IO.c
  Matras.c:77:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
     77 | main(argc,argv)
        | ^~~~
  Matras.c: In function ‘main’:
  Matras.c:126:3: warning: implicit declaration of function ‘Set_AAnum’ [-Wimplicit-function-declaration]
    126 |   Set_AAnum();
        |   ^~~~~~~~~
  Matras.c:390:27: warning: zero-length gnu_printf format string [-Wformat-zero-length]
    390 |         sprintf(envscfile,"");
        |                           ^~
  Matras.c:431:23: warning: zero-length gnu_printf format string [-Wformat-zero-length]
    431 |   sprintf(PAR.COMMAND,"");
        |                       ^~
  Matras.c:436:29: warning: implicit declaration of function ‘Get_Date_String’; did you mean ‘Get_Time_String’? [-Wimplicit-function-declaration]
    436 |   printf("#<DATE> \"%s\"\n",Get_Date_String());
        |                             ^~~~~~~~~~~~~~~
        |                             Get_Time_String
  Matras.c:436:22: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
    436 |   printf("#<DATE> \"%s\"\n",Get_Date_String());
        |                     ~^      ~~~~~~~~~~~~~~~~~
        |                      |      |
        |                      char * int
        |                     %d
  Matras.c:442:10: warning: too many arguments for format [-Wformat-extra-args]
    442 |   printf("# QueFile \"%s\" LibFile \"%s\"\n",MODE,QueFile,LibFile);
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Matras.c:498:4: warning: implicit declaration of function ‘Pairwise_3D_Alignment’ [-Wimplicit-function-declaration]
    498 |    Pairwise_3D_Alignment(&proA,&proB,&DmapA,&DmapB,&AHead,&SHead,inalifile,inssefile);
        |    ^~~~~~~~~~~~~~~~~~~~~
  Matras.c:502:4: warning: implicit declaration of function ‘mainPD’; did you mean ‘main’? [-Wimplicit-function-declaration]
    502 |    mainPD(&proA, &proB, AHead.next, inalifile ); /* JR ProtDeform */
        |    ^~~~~~
        |    main
  Matras.c:529:5: warning: implicit declaration of function ‘Output_Path_Horizontal_ClustalW’; did you mean ‘Output_Path_Horizontal_HTMLcolor’? [-Wimplicit-function-declaration]
    529 |     Output_Path_Horizontal_ClustalW(&proA,&proB,an,outclwfile);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        |     Output_Path_Horizontal_HTMLcolor
  Matras.c:726:6: warning: implicit declaration of function ‘Cal_Raw_MeanSD_Llist’; did you mean ‘Cal_Raw_Zscore_Llist’? [-Wimplicit-function-declaration]
    726 |      Cal_Raw_MeanSD_Llist(&ALibHead,&Mean,&SD);
        |      ^~~~~~~~~~~~~~~~~~~~
        |      Cal_Raw_Zscore_Llist
  Matras.c:512:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
    512 |     sprintf(OutHead,"%s%d",OheadStr,an->num);
        |                          ^
  Matras.c:512:5: note: ‘sprintf’ output between 2 and 139 bytes into a destination of size 128
    512 |     sprintf(OutHead,"%s%d",OheadStr,an->num);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Matras.c:587:43: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 113 and 240 [-Wformat-overflow=]
    587 |      { sprintf(command,"perl %s/rotSTR.pl %s.mat %s -nc A -S B > %s.pdb",
        |                                           ^~
    588 |              BASE_DIR,OutHead,proAfile,OutHead);
        |                       ~~~~~~~              
  Matras.c:587:8: note: ‘sprintf’ output between 40 and 484 bytes into a destination of size 256
    587 |      { sprintf(command,"perl %s/rotSTR.pl %s.mat %s -nc A -S B > %s.pdb",
        |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    588 |              BASE_DIR,OutHead,proAfile,OutHead);
        |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Matras.c:590:62: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 33 and 223 [-Wformat-overflow=]
    590 |        sprintf(command,"perl %s/rotSTR.pl - %s -nc B -S B >> %s.pdb",BASE_DIR,proBfile,OutHead);
        |                                                              ^~                        ~~~~~~~
  Matras.c:590:8: note: ‘sprintf’ output between 38 and 355 bytes into a destination of size 256
    590 |        sprintf(command,"perl %s/rotSTR.pl - %s -nc B -S B >> %s.pdb",BASE_DIR,proBfile,OutHead);
        |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Matras.c:594:43: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 113 and 240 [-Wformat-overflow=]
    594 |      { sprintf(command,"perl %s/rotSTR.pl %s.mat %s -nc A -S P -ch %c -H W > %s.pdb",
        |                                           ^~
    595 |            BASE_DIR,OutHead,proAfile,proA.chain,OutHead);
        |                     ~~~~~~~                
  Matras.c:594:8: note: ‘sprintf’ output between 51 and 495 bytes into a destination of size 256
    594 |      { sprintf(command,"perl %s/rotSTR.pl %s.mat %s -nc A -S P -ch %c -H W > %s.pdb",
        |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    595 |            BASE_DIR,OutHead,proAfile,proA.chain,OutHead);
        |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Matras.c:597:73: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 23 and 213 [-Wformat-overflow=]
    597 |       sprintf(command,"perl %s/rotSTR.pl - %s -nc B -S P -ch %c -H W>> %s.pdb",
        |                                                                        ^~
  
    598 |         BASE_DIR,proBfile,proB.chain,OutHead);
        |                                      ~~~~~~~                            
  
  Matras.c:597:8: note: ‘sprintf’ output between 48 and 365 bytes into a destination of size 256
    597 |        sprintf(command,"perl %s/rotSTR.pl - %s -nc B -S P -ch %c -H W>> %s.pdb",
        |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    598 |          BASE_DIR,proBfile,proB.chain,OutHead);
        |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Amino.c: In function ‘Amino_Name’:
  Amino.c:104:11: warning: implicit declaration of function ‘strncmp’ [-Wimplicit-function-declaration]
    104 |       if (strncmp(t,"ALA",3)==0)  r = 'A';
        |           ^~~~~~~
  Amino.c:104:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    104 |       if (strncmp(t,"ALA",3)==0)  r = 'A';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:105:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    105 |  else if (strncmp(t,"GLU",3)==0)  r = 'E';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:106:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    106 |  else if (strncmp(t,"GLN",3)==0)  r = 'Q';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:107:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    107 |  else if (strncmp(t,"ASP",3)==0)  r = 'D';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:108:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    108 |  else if (strncmp(t,"ASN",3)==0)  r = 'N';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:109:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    109 |  else if (strncmp(t,"LEU",3)==0)  r = 'L';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:110:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    110 |  else if (strncmp(t,"GLY",3)==0)  r = 'G';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:111:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    111 |  else if (strncmp(t,"LYS",3)==0)  r = 'K';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:112:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    112 |  else if (strncmp(t,"SER",3)==0)  r = 'S';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:113:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    113 |  else if (strncmp(t,"VAL",3)==0)  r = 'V';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:114:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    114 |  else if (strncmp(t,"ARG",3)==0)  r = 'R';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:115:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    115 |  else if (strncmp(t,"THR",3)==0)  r = 'T';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:116:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    116 |  else if (strncmp(t,"PRO",3)==0)  r = 'P';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:117:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    117 |  else if (strncmp(t,"ILE",3)==0)  r = 'I';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:118:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    118 |  else if (strncmp(t,"MET",3)==0)  r = 'M';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:119:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    119 |  else if (strncmp(t,"PHE",3)==0)  r = 'F';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:120:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    120 |  else if (strncmp(t,"TYR",3)==0)  r = 'Y';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:121:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    121 |  else if (strncmp(t,"CYS",3)==0)  r = 'C';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:122:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    122 |  else if (strncmp(t,"TRP",3)==0)  r = 'W';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:123:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    123 |  else if (strncmp(t,"HIS",3)==0)  r = 'H';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:124:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    124 |  else if (strncmp(t,"UNK",3)==0)  r = 'u';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:125:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    125 |  else if (strncmp(t,"ACE",3)==0)  r = 'a';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  Amino.c:126:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
    126 |  else if (strncmp(t,"FOR",3)==0)  r = 'f';
        |                           ^
  <built-in>: note: built-in ‘strncmp’ declared here
  GotohDPdis.c: In function ‘GotohDP_Dscore_Iterative’:
  GotohDPdis.c:202:3: warning: implicit declaration of function ‘ScoreDistanceSPair’; did you mean ‘ScoreDistanceS’? [-Wimplicit-function-declaration]
    202 |   ScoreDistanceSPair(proA,proB,an,DmapA,DmapB);
        |   ^~~~~~~~~~~~~~~~~~
        |   ScoreDistanceS
  GotohDPdis.c: In function ‘GotohDP_Dscore’:
  GotohDPdis.c:223:33: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
    223 |   { printf("#ERROR:PRE.MaxNali %s is less than Nali %d\n",PRE.MaxNali,an->Nali);
        |                                ~^                         ~~~~~~~~~~~
        |                                 |                            |
        |                                 char *                       int
        |                                %d
  DiffStr.c: In function ‘Number_Sec’:
  DiffStr.c:202:5: warning: type of ‘sym’ defaults to ‘int’ [-Wimplicit-int]
    202 | int Number_Sec(sym,Nstr)
        |     ^~~~~~~~~~
  SecStrEle.c: In function ‘Output_SSE_PDB’:
  SecStrEle.c:355:13: warning: too many arguments for format [-Wformat-extra-args]
    355 |  fprintf(fp,"REMARK tFactor : 0 for Cend of SSE, 200 for  helix, 100 for sheet\n",pr->pname);
        |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ScoreENV.c: In function ‘Number_Sec’:
  ScoreENV.c:313:5: warning: type of ‘sym’ defaults to ‘int’ [-Wimplicit-int]
    313 | int Number_Sec(sym,Nstr)
        |     ^~~~~~~~~~
  ScoreENV.c: In function ‘Read_Env_Score’:
  ScoreENV.c:264:22: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
    264 |  sprintf(Fname,"%s/%s",SCORE_DIR,fname);
        |                      ^
  ScoreENV.c:264:2: note: ‘sprintf’ output 2 or more bytes (assuming 129) into a destination of size 128
    264 |  sprintf(Fname,"%s/%s",SCORE_DIR,fname);
        |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  BuildUpL.c: In function ‘Build_Up_LL’:
  BuildUpL.c:256:2: warning: implicit declaration of function ‘Merge_Sort_Double_Linked_List’ [-Wimplicit-function-declaration]
    256 |  Merge_Sort_Double_Linked_List(head,'R');
        |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  BuildUpL.c: In function ‘Read_SSE_Alignment’:
  BuildUpL.c:677:4: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
    677 |    Get_Part_Of_Line(num1,word1,1,strlen(word1));
        |    ^~~~~~~~~~~~~~~~
  OutAln.c: In function ‘Write_Rasmol_Color_Alignment’:
  OutAln.c:564:34: warning: implicit declaration of function ‘Get_Date_String’ [-Wimplicit-function-declaration]
    564 |  fprintf(fp,"# DATE      '%s'\n",Get_Date_String());
        |                                  ^~~~~~~~~~~~~~~
  OutAln.c:564:28: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
    564 |  fprintf(fp,"# DATE      '%s'\n",Get_Date_String());
        |                           ~^     ~~~~~~~~~~~~~~~~~
        |                            |     |
        |                            |     int
        |                            char *
        |                           %d
  OutAln.c: In function ‘Write_Rasmol_Color_Alignment_Each_Protein’:
  OutAln.c:715:27: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
    715 |  fprintf(fp,"# DATE      %s\n",Get_Date_String());
        |                          ~^    ~~~~~~~~~~~~~~~~~
        |                           |    |
        |                           |    int
        |                           char *
        |                          %d
  OutAln.c:731:10: warning: implicit declaration of function ‘Ncompare’ [-Wimplicit-function-declaration]
    731 |  Ncomp = Ncompare(a);
        |          ^~~~~~~~
  OutAln.c: In function ‘Write_Molscript_Alignment_Each_Protein’:
  OutAln.c:880:27: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
    880 |  fprintf(fp,"! DATE      %s\n",Get_Date_String());
        |                          ~^    ~~~~~~~~~~~~~~~~~
        |                           |    |
        |                           |    int
        |                           char *
        |                          %d
  OutAln.c:905:35: warning: implicit declaration of function ‘Remove_Space’ [-Wimplicit-function-declaration]
    905 |        if (OutProteinType == 'A') Remove_Space(rsta,pA->Rnum[a->nalA[i]]);
        |                                   ^~~~~~~~~~~~
  OutAln.c: In function ‘Find_nal’:
  OutAln.c:962:5: warning: type of ‘q’ defaults to ‘int’ [-Wimplicit-int]
    962 | int Find_nal(q,Nali,nalA)
        |     ^~~~~~~~
  OutAln.c: In function ‘Output_Alignment_Information’:
  OutAln.c:1058:2: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
   1058 |  Get_Part_Of_Line(ln,pA->compnd,0,40);
        |  ^~~~~~~~~~~~~~~~
  StrLibL.c: In function ‘Read_Library_List’:
  StrLibL.c:75:5: warning: implicit declaration of function ‘Get_First_Field’ [-Wimplicit-function-declaration]
     75 |     Get_First_Field(name,tax,buffer);
        |     ^~~~~~~~~~~~~~~
  StrLibL.c: In function ‘Check_Library_List’:
  StrLibL.c:113:3: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
    113 |   Get_Part_Of_Line(dir,bn->Name,1,2);
        |   ^~~~~~~~~~~~~~~~
  OutLibL.c: In function ‘Output_Library_ClustalW’:
  OutLibL.c:234:4: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
    234 |    Get_Part_Of_Line(ln,bn->sim->Name,0,16);
        |    ^~~~~~~~~~~~~~~~
  LlistIO.c: In function ‘Read_BSSP_File_LinearList’:
  LlistIO.c:161:2: warning: implicit declaration of function ‘Set_SSE’ [-Wimplicit-function-declaration]
    161 |  Set_SSE(pr);
        |  ^~~~~~~
  LlistIO.c:162:2: warning: implicit declaration of function ‘Set_Dis_bwn_SSE’ [-Wimplicit-function-declaration]
    162 |  Set_Dis_bwn_SSE(pr,'C');
        |  ^~~~~~~~~~~~~~~
  LlistIO.c: In function ‘Translate_BSSP_File_LinearList’:
  LlistIO.c:218:51: warning: implicit declaration of function ‘tolower’ [-Wimplicit-function-declaration]
    218 |             if (X->line[75]=='C') pr->Seq[Rnum] = tolower(pr->Seq[Rnum]);  /* for CIS conf */
        |                                                   ^~~~~~~
  PairAli.c: In function ‘Pairwise_3D_Alignment’:
  PairAli.c:188:3: warning: implicit declaration of function ‘Set_Value_AlignNode’; did you mean ‘Tail_Value_AlignNode’? [-Wimplicit-function-declaration]
    188 |   Set_Value_AlignNode(Ahead,'S');    /* JR  It was  D */
        |   ^~~~~~~~~~~~~~~~~~~
        |   Tail_Value_AlignNode
  PairAli.c:189:3: warning: implicit declaration of function ‘Merge_Sort_Double_Linked_List’ [-Wimplicit-function-declaration]
    189 |   Merge_Sort_Double_Linked_List(Ahead,'R');
        |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  IO.c: In function ‘Read_BSSP_File’:
  IO.c:705:3: warning: implicit declaration of function ‘Set_SSE’ [-Wimplicit-function-declaration]
    705 |   Set_SSE(pr);
        |   ^~~~~~~
  IO.c:706:3: warning: implicit declaration of function ‘Set_Dis_bwn_SSE’ [-Wimplicit-function-declaration]
    706 |   Set_Dis_bwn_SSE(pr,'C');
        |   ^~~~~~~~~~~~~~~
  IO.c: In function ‘Read_Sequence’:
  IO.c:886:13: warning: implicit declaration of function ‘isalpha’ [-Wimplicit-function-declaration]
    886 |    else if (isalpha(sym)!=0)
        |             ^~~~~~~
  IO.c: In function ‘Read_Matras_Environment_File’:
  IO.c:87:23: warning: ‘%s’ directive writing up to 63 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
     87 |   sprintf(Matfile,"%s/%s",homedir,matfile);
        |                       ^~          ~~~~~~~
  IO.c:87:3: note: ‘sprintf’ output between 2 and 192 bytes into a destination of size 128
     87 |   sprintf(Matfile,"%s/%s",homedir,matfile);
        |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  IO.c: In function ‘Read_PDB_File’:
  IO.c:378:20: warning: ‘%s’ directive writing up to 3 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
    378 |  sprintf(Fname,"%s/%s/%s",PDB_DIR,dir,fname);
        |                    ^~             ~~~
  IO.c:378:2: note: ‘sprintf’ output 3 or more bytes (assuming 133) into a destination of size 128
    378 |  sprintf(Fname,"%s/%s/%s",PDB_DIR,dir,fname);
        |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  g++ -c  -g vector.cpp TransSeq.cpp Geometry.cpp WriteDeformPDB.cpp Evaluation.cpp  -w
  Geometry.cpp:30:31: error: ‘<unnamed enum> GEOMETRY’, declared using unnamed type, is used but never defined [-fpermissive]
     30 | extern enum { RIGID, AFFINE } GEOMETRY;
        |                               ^~~~~~~~
  WriteDeformPDB.cpp:16:31: error: ‘<unnamed enum> GEOMETRY’, declared using unnamed type, is used but never defined [-fpermissive]
     16 | extern enum { RIGID, AFFINE } GEOMETRY;
        |                               ^~~~~~~~
  make: *** [Makefile:125: ../ProtDeform] Error 1
  
  ```
  
  I've contacted the program developers about this, but am still waiting for answer from them.
  
  Can you help?
  
  EDIT1:
  ox
  I've checked
  
  Ubuntu 16.04 on virtualbox
  
  Ubuntu 20.04 with i7
  
  Ubuntu 20.04 with Ryzen 9
  
  same error...
  
  EDIT 2:
  
  ```
  I have found hidden file .matras:
  ###############################
  ### MATRAS ENVIRONMENT FILE ###
  ###############################
  
  BASE_DIR .
  SCORE_DIR  data_sc/ROM-04JAN29
  TMP_DIR    .
  BSSP_DIR  /DB/BSSP
  PDB_DIR   /DB/PDB
  
  ```
  
  I'm checking to see if it simply requires PDB
  
  **Tags:** proteins, protein-structure, bash, perl
  
  > **Comments:**
  > **username_1**: What is ProtDeform? Why are you trying to use it? Can you give any additional context around your problem that would help in finding a solution?  
  > **username_0**: @username_1 I add some information. Yes, still waiting for answer :/  
  > **username_2**: The tool is more than 10 years old, without documentation for compilation and without any documentation towards software versions. The paper has a single citation, indication it never has been adopted by the community. Hence, find something else that actually works. Not what you want to hear, I know.  
  > **username_3**: is this webserver giving any result with your input https://bioinfo.uib.es/~recerca/ProtDeform/  
  > **username_3**: are you trying to run or install the software ??  
  > **username_0**: @username_3 install to run :)  
  
  ---
  
  ## 0 answers
  
  