AMBER Archive (2009)

Subject: Re: [AMBER] gaussian 98 input/output for antechamber/resp

From: Karl Kirschner (kkirsch_at_scai.fraunhofer.de)
Date: Thu Aug 13 2009 - 01:57:41 CDT

On Wednesday 12 August 2009 20:41, wong105_at_llnl.gov wrote:
> Dear Amber users;
>
> I'm using antechamber (Amber 8)/gaussian 98 to calculate charges
> for a ligand. I start with a mol2 file and obtain from antechamber a
> gaussian input file. The gaussian input file looks like this:
>
>
> --Link1--
> %chk=MOL
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
>
> remark line goes here
>
> 1 1
> N 1.2410 -4.7650 42.5820
> C 0.1340 -4.4500 43.3000
>
> I made the assumption that I could take this input file to obtain the
> electrostatic potential for RESP. I also noticed the "opt" keyword,
> which, I assumed served the purpose of relaxing the molecule to obtain
> a reasonable response.
>
> Two observations:
>
> 1) I noticed that the electrostatic potential data is only printed
> for the first point in the optimization, rather than the final
> geometry. That would seem to defeat the point of the optimization.
>
> 2) After 10,000 points, one gets **** for the point number:
>
> ESP Fit Center 9998 is at -1.493521 -3.825592 -3.033347
> ESP Fit Center 9999 is at -1.062486 -3.825592 -3.033347
> ESP Fit Center **** is at -0.657445 -3.678169 -3.033347
> ESP Fit Center **** is at -0.327253 -3.401105 -3.033347
> ESP Fit Center **** is at -0.111735 -3.027817 -3.033347
>
> Does the resp program know how to deal with this? It does not yield
> show any errors when I run it to calculate charges, but I wonder if it
> ignores these points. Perhaps others have addressed these points in
> the past, but a quick google search did not yield an obvious answer.
> Any ideas?
>
> Thanks;
>
> -Sergio
>

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