Replying to myself.
If you write a pdb with x, then use it the way you describe,
you get the behavior you indicated. Something is going
wrong. What leap has after the combine is different from
what it has from reading the pdb file:
source leaprc.ff99SB
x = combine {ACE THR NME}
savepdb x test.pdb
savemol2 x test.mol2 0
y = loadmol2 test.mol2
quit
versus
source leaprc.ff99SB
x = loadpdb test.pdb
savemol2 x test.mol2 0
y = loadmol2 test.mol2
quit
One thing I noticed is that x from combine has TER cards in
the written pdb file, whereas the pdb file I used in the
second case had the TER cards removed. (But the behavior
you described happened with or without the TER cards.)
Puzzled,
Bud
On Nov 10, 2011, at 3:09 PM, M. L. Dodson wrote:
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> 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
>
>
>
> <test.mol2><test.log><test.in>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 10 2011 - 14:00:02 PST
