On Fri, Apr 1, 2011 at 10:57 AM, Mark M Huntress <markmh.bgsu.edu> wrote:
> Hi, I am generating parameters (.prmtop file) for an organic molecule, and
> I am curious about the way to make the library file, specifically, should I
> load the NEWPDB.PDB file that is generated by antechamber? (Should I include
> the commands that are commented out?) I tried it both ways, and there were
> differences in the .lib files, and in the .prmtop files between the two
> methods. Is one of them WRONG? Or could I use either method? Thanks.
>
Load the prepin file. Another suggestion I have, perhaps, is to use the
mol2 file format instead of the amber prep format.
To save the OFF file, use:
loadamberprep Eresp.prepin
saveoff *MOL* Eresp.lib
Here, *MOL* is the residue name in your prepin file. You can use the "list"
command after you load it in leap to see which residue was added.
I would suggest doing this in its own leap session so you don't have other
stuff confusing things.
Hope this helps,
Jason
> module load amber9
> $AMBERHOME/exe/antechamber -i Eresp.log -fi gout -nc 1 -o Eresp.prepin -fo
> prepi -c resp -s 2 #(NEWPDB.PDB has been generated now from the log file)
> parmchk -i Eresp.prepin -f prepin -o Eresp.frcmod -p gaff.dat
> $AMBERHOME/exe/tleap
> source leaprc.gaff
> loadamberprep Eresp.prepin
> mods = loadamberparams Eresp.frcmod
> #mol = loadpdb NEWPDB.PDB #?????????????????
> #saveoff mol Eresp.lib
> saveoff MOL Eresp.lib
>
>
> module load amber9
> $AMBERHOME/exe/tleap
> source leaprc.ff03
> source leaprc.gaff
> loadoff moh.lib
> loadoff Eresp.lib
> mods = loadamberparams Eresp.frcmod
> mol = loadpdb Erespgood.pdb
> saveamberparm mol Eresp.prmtop Eresp.crd
> quit
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Apr 01 2011 - 11:30:03 PDT
