Excuse me for jumping in.
Your statement is not correct in the general case. Maybe it
is for your test.pdb.
See attachments.
Command line was: tleap -f test.in > test.log
Bud Dodson
On Nov 10, 2011, at 1:26 PM, Jan-Philip Gehrcke wrote:
> Hello,
>
> in leap you can use any test.pdb file as input and try
>
>> source leaprc.ff99SB
>> x = loadpdb test.pdb
>> savemol2 x out.mol2 0
>> y = loadmol2 out.mol2
>
> which will result in something like
>
>> Loading PDB file: ./test.pdb
>> [...]
>> Writing mol2 file: out.mol2
>> [...]
>> Loading Mol2 file: ./out.mol2
>> Reading MOLECULE named [...]
>> Fatal Error: last line read: [...]
>
> This is because the molecule name is not written by leap and then it is
> expected during parsing. This is correct, since the molecule name is
> required by the MOL2 format specification.
>
> Now, I've quickly looked into the code of mol2File.c.
>
> `sContainerName((CONTAINER) uUnit)` is used to get the object's name.
> But it seems to be broken and returns an "empty string" which results in
> the problem described above.
>
> It is really hard to figure out how to get the object's name back. After
> some minutes I gave up. The code in mol2File.c itself is badly
> structured and I don't know if it's worth investing time in it. Besides
> fixing the molecule name issue, there is more to do.. for example it
> prints "Truncating residue name for PDB format: CLEU -> CLE" (and then
> nevertheless writes "CLEU" to the MOL2 file).
>
> To make a long story short.. a quick fix would be to just write a
> default molecule name to any MOL2 file in order to at least stick to the
> MOL2 format specs. This change worked for me:
>
>
> --- src/leap/mol2File.c.old 2011-11-10 20:08:23.081930188 +0100
> +++ src/leap/mol2File.c 2011-11-10 20:09:22.043721048 +0100
> .. -288,7 +288,7 ..
> iResidueCount = zUnitIOAmberOrderResidues( uUnit );
>
>
> -strcpy( sTemp, sContainerName((CONTAINER) uUnit));
> +//strcpy( sTemp, sContainerName((CONTAINER) uUnit));
>
> iCount = 0;
> lTemp = lLoop((OBJEKT) uUnit, BONDS);
> .. -302,7 +302,7 ..
>
> iBondCount = iCount;
>
> -fprintf(fOut, "%s\n", sTemp) ;
> +fprintf(fOut, "molecule_name\n") ;
> fprintf(fOut, "%5d %5d %5d 0 1 \n",
> iAtomCount,iBondCount,iResidueCount) ;
> fprintf(fOut, "SMALL\n");
> fprintf(fOut, "USER_CHARGES\n");
>
>
> -->
>
>> Loading PDB file: ./test.pdb
>> [...]
>> Writing mol2 file: out.mol2
>> [...]
>> Loading Mol2 file: ./out.mol2
>> Reading MOLECULE named molecule_name
>
>
>
> Maybe it's useful.
>
> Jan-Philip
>
>
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--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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- application/octet-stream attachment: test.mol2
- application/octet-stream attachment: test.log
- application/octet-stream attachment: test.in
Received on Thu Nov 10 2011 - 13:30:04 PST
