Hello Amber users, Matt and Francois,
Thanks for your inputs. Based on the comments the following strategy is what
I've come up with,
1. Take the pdb file, feed it to NWChem and get the optimized geometry.
2. Take the optimized pdb file, feed it to antechamber and get the RESP
charges, parameter and topology files.
I don't have access to Gaussian so I'll have to use antechamber's charges
for now.
Thanks for all your inputs.
On 1/19/07, mernst.tricity.wsu.edu <mernst.tricity.wsu.edu> wrote:
>
> > Quoting mernst.tricity.wsu.edu:
> >
> >> I do not know what version of NWChem you are using. NWChem at least
> >> version 4.5-4.7 does
> >> not properly implement RESP, though it can give deceptively
> >> good-looking results on some
> >> molecules. I will guess you want RESP, not plain ESP, as that's how
> >> AMBER charges were
> >> assigned. NWChem is not suitable for RESP. I know that NWChem 5.0
> >> has significantly
> >> changed its RESP charge calculations, but they too were flawed
> >> (though in a different
> >> way) when I used it in beta. If you want to verify that your
> >> software and methods are
> >> reasonable, obtain the original RESP papers and confirm that you can
> >> reproduce results
> >> for simple cases like butane and n-methylacetamide. NWChem seemed to
> >> give especially
> >> unreasonable results on butane when I was doing my own verifications.
> >
> > Here, is it not possible to ask to NWChem to only (i) optimize a
> > structure (ii) compute the MEP and NOT derive the charges; letting the
> > RESP program doing the fitting step to generate RESP or ESP charge
> > values ?
> >
> > Did you try to compare the MEP generated by Gaussian, and that
> > generated by NWChem ? Are they identical ? Thanks, Francois
> That seems like a reasonable approach. I think it is NWChem's built-in
> fitting with
> restraints/constraints that is bad, not its underlying quantum chemistry.
> I discovered
> RED II as I was looking for the source of the NWChem trouble, and
> immediately began
> using it with GAMESS. I did not take the time to parse the NWChem output
> for use with
> the external RESP program.
>
> Matt Ernst
>
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Received on Wed Jan 31 2007 - 06:07:07 PST
