AMBER Archive (2008)

Subject: AMBER: resp charges in parameterization

From: Mark M Huntress (markmh_at_bgsu.edu)
Date: Wed Nov 12 2008 - 10:24:55 CST

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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