>> The zn-complex.mol2 file seems to be missing a name:
>>
>> .<TRIPOS>MOLECULE
>>
>> 52 49 1 0 0
>>
>> The blank line after the MOLECULE line should have something there.
>> Try putting something in there and then see if leap loads it
>
> Actually now that I look again, just adding the name after the
> MOLECULE line won't work since all of the ATOM lines are missing the
> residue name as well:
>
> 1 N -0.3780 1.8940 -1.9700 n3 1 -0.856800
>
> There should be something after the 7th column. So hopefully the '-rn'
> flag of antechamber works, otherwise you would need to manually edit
> all the ATOM lines. The file should look like this:
>
> .<TRIPOS>MOLECULE
> MOL
> 52 49 1 0 0
> SMALL
> bcc
>
>
> .<TRIPOS>ATOM
> 1 N -0.3780 1.8940 -1.9700 n3 1 MOL -0.856800
> ...
> etc
>
This works. Thanks for looking at this, Dan!
Using antechamber with the -rn flag does the trick. However, the manual states that the default residue name is MOL if it is not present in the input file. I didn't test this with another pdb but either this is a bug or a wrong statement in the manual which should be fixed.
All the best,
Andy
PS: The world is so much easier if we only have nuclei and electrons ;)
> -Dan
>
>> correctly. I'm not sure why antechamber didn't just put a name there
>> (usually its something like MOL). You could also try rerunning
>> antechamber with the -rn <residue_name> option to see if that will
>> give it a name.
>>
>> -Dan
>>
>> On Tue, Jul 27, 2010 at 9:17 PM, Andreas Goetz <agoetz.sdsc.edu> wrote:
>>> Hi All,
>>>
>>> I have a pdb file of a Zn complex for which I want to generate Amber inpcrd/prmtop files. I used antechamber and parmchk to generate mol2 and frcmod files to be used with leap. However, leap fails to read the mol2 file which antechamber generates. It is my understanding that leap should be able to load any mol2 file which has been generated by antechamber.
>>>
>>> This is what I did:
>>>
>>> antechamber -i zn-complex.pdb -fi pdb -o zn-complex.mol2 -fo mol2 -c bcc -s 2
>>> parmchk -i zn-complex.mol2 -f mol2 -o zn-complex.frcmod
>>> tleap
>>> > source leaprc.gaff
>>> > mod = loadAmberParams zn-complex.frcmod
>>> > foo = loadMol2 zn-complex.mol2
>>> Loading Mol2 file: ./zn-complex.mol2
>>> Reading MOLECULE named 52 49 1 0 0
>>> Fatal Error: last line read: 1 N -0.3780 1.8940 -1.9700 n3 1 -0.856800
>>>
>>> Same happens in xleap.
>>>
>>> Input, output and log files can be found at http://www.wmd-lab.org/agoetz/acmol2problem
>>>
>>> Can someone who knows antechamber and leap have a look at why this is not working?
>>> Thanks for any help.
>>>
>>> All the best,
>>> Andy
>>>
>>> --
>>> Dr. Andreas W. Goetz
>>> San Diego Supercomputer Center
>>> Tel : +1-858-822-4771
>>> Email: agoetz.sdsc.edu
>>> Web : www.awgoetz.de
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>
>>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
--
Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
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Received on Tue Jul 27 2010 - 23:00:03 PDT
