VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Jan 16 2011 - 17:12:10 CST

For what it's worth, I tried running your input with Gaussian 09 and got the following error pretty quickly

 Small interatomic distances encountered: 23 3 30 13
 Problem with the distance matrix.

Nothing about charge or multiplicity though.

On Jan 12, 2011, at 12:13 PM, Ali, Rejwan wrote:

> Seems like my previous attachment didn’t go thru outlook filter. Here is the g03 input file. Thanks.
>
> Ali
>
> From: Ali, Rejwan
> Sent: Wednesday, January 12, 2011 12:55 PM
> To: 'Jacqueline Cawthray'
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: RE: vmd-l: Issues with Paratools and Gaussian
>
> Hi,
>
> Attached find please Gaussian input file generated by VMD 1.86. I’m using g03 version of Gaussian. Thanks.
>
> Ali
>
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Jacqueline Cawthray
> Sent: Tuesday, January 11, 2011 6:10 PM
> To: Ali, Rejwan
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Issues with Paratools and Gaussian
>
> Hi
>
> It might be helpful if you include the input file generated by Paratools and indicate the version of Gaussian you are using. It would make it easier to see what the problem is then.
>
> Regards
> Jacquie
>
> On Tue, Jan 11, 2011 at 12:51 PM, Ali, Rejwan <rejwan.ali_at_mssm.edu> wrote:
> In order to run a NAMD simulation of a receptor-ligand structure, I'm having some issues with VMD Paratools and Gaussian.
> The ligand structure is apperantly fine as viewed in VMD. However, Gaussian complains about the input file as generated
> by Paratools for the ligand for charge and multiplicity. Any clue to how a Gaussian compatible input file can be written Paratools
> so that after Gaussian Geomery optmization the log file can be imported in Paratools to generate
> parameters for the ligand ? We are interested to use Charmm force field. Thank you.
>
> Rejwan Ali
>
>
>
> --
>
> <s-7_h_ad.txt>