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.
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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Received on Fri Apr 01 2011 - 11:00:03 PDT
