AMBER Archive (2008)

Subject: Re: AMBER: resp charges in parameterization

From: steinbrt_at_rci.rutgers.edu
Date: Wed Nov 12 2008 - 10:44:17 CST

Hi,

you can look at the charges resp assigned to your molecule either in the
prep file that you created (in the last or next to last column) or, after
loading it in xleap you can use the graphical interface to check them:

xleap
>loadamberprep aze-H.prep
>edit MOL

(the name of your unit is probably MOL, since thats the antechamber
default and your command did not overwrite it)

Under display in the edit window select charges.

The charges for each atom will also be in the prmtop file, but they are
multiplied by a constant into an internal amber format, so thats not the
best place to check them.

Regards,

Thomas

On Wed, November 12, 2008 11:24 am, Mark M Huntress wrote:
> 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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Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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