Hi,
I used antechamber to parametrize my unconventional protein, and I used gaussian to calculate resp charges first:,
HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6)
Output file: aze-H.log
Then I used antechamber:
antechamber –i aze-H.log –fi gout –nc 1 –o aze-H.prep –fo prepc –c resp –s 2
parmchk –i aze-H.prep –f prepc –o aze-H.frcmod – p gaff.dat
and eventually generated prmtop and crd files:
> saveamberparm mol 2G7B-na-aze-solv.prmtop 2G7B-na-aze-solv.crd
> savepdb mol 2G7B-na-aze-solv.pdb
SO MY QUESTION IS THIS:
I want to check the resp charges to see if they are reasonable. Should I be able to find them listed somewhere in the prmtop or crd, (one of the MD input files), or does this procedure just utilize the resp information in the parameter builiding process, integrating the resp info into the parameters?
Thanks,
Mark
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Received on Fri Dec 05 2008 - 14:34:10 PST
