On Tue, Jul 27, 2010 at 11:36 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
-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
>>
>>
>>
>>
>>
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>>
>
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Received on Tue Jul 27 2010 - 21:00:04 PDT
