VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Mar 26 2019 - 10:32:10 CDT

Just to confirm what Joao said - apperently I spoke too soon. CHARMM-GUI
does not seem able to handle the new CGenFF str files either.

For the time being you will have to use CHARMM directly if you want to
construct CGenFF systems containing lonepairs.

On Tue, Mar 26, 2019 at 10:03 AM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> Hi Aravinda,
>
>
>
> You are correct. Psfgen does not support this halogens colinear lonepairs,
> but efforts are being made to change that. I cannot say for sure when such
> lonepairs supporting psfgen version will be available, but it is something
> that is on its way.
>
>
>
> To be honest, I am not aware of a tool that can prepare psf files
> containing this colinear lonepairs), besides charmm package itself. I
> believe that charm-gui is not doing it so far.
>
>
>
> Probably some other user might knows a tool that can do it.
>
>
>
> Best
>
>
>
> João
>
>
>
>
>
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
>
> http://www.ks.uiuc.edu/~jribeiro/
>
> jribeiro_at_illinois.edu
>
> +1 (217) 3005851
>
>
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of Aravinda Munasinghe <
> aravinda1879_at_gmail.com>
> *Date: *Monday, March 25, 2019 at 9:38 PM
> *To: *VMD Mailing LIst <vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: VMD psfgen lonepair handling
>
>
>
> Dear VMD users,
>
> I want to generate a molecule with a CL bond. And to get the topology
> information, I have used the new version of the parmchk (which uses CGenFF
> 4.0). However, since the new version supports the lonepair for halogens, my
> STR file has the following line
>
> LONEPAIR COLI LP1 CL C2 DIST 1.6400 SCAL 0.0
>
> However, when the psfgen reading the STR file, it throws the following
> error,
>
> psfgen) ERROR! FAILED TO RECOGNIZE LONEPAIR. Line 69: LONEPAIR COLI LP1
> CL C2 DIST 1.6400 SCAL 0.0
>
> Does this mean VMD psfgen still does not support lonepair implementation
> for NAMD input generation?. If that is so, what other ways can I
> incorporate the lone pair related topology to the psf file?.
>
>
>
> Best,
>
>
>
> --
>
> Aravinda Munasinghe,
>
>
>