VMD-L Mailing List

From: Jeevan Patra (jeevanpatra96_at_gmail.com)
Date: Mon Jul 31 2023 - 12:49:20 CDT

Matt, I have a protein-ligand complex in pdb format. Can this whole complex
can be generated with CHARMM force field?

On Sun, 30 Jul, 2023, 11:33 pm Sinclair, Matt, <mts7_at_illinois.edu> wrote:

> Jeevan,
>
>
>
> This is likely because the CHARMM force field does not have parameters
> for the ligand. You will need to obtain these parameters by using a tool
> such as CGENFF (via the ligand modeler on CHARMM-GUI or paramchem web
> server). Without parameters for your ligand NAMD will crash every time you
> try to run it, hence the parameter error you are receiving.
>
>
>
> Best,
>
> Matt Sinclair
>
>
>
> *Graduate Student, Tajkhorshid Lab*
>
> *Theoretical & Computational Biophysics Group*
>
> *NIH Center for Macromolecular Modeling & Visualization*
>
> *Department of Biochemistry, University of Illinois Urbana-Champaign*
>
>
>
> *From: *owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Jeevan Patra <jeevanpatra96_at_gmail.com>
> *Date: *Sunday, July 30, 2023 at 11:32 AM
> *To: *vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: QwikMD - Steered Molecular Dynamics Query
>
> I am trying to perform steered molecular dynamics of a protein-ligand
> complex using QwikMD. During the structure check, the ligand was annotated
> as hetero and the red warning message was a topological parameter error. I
> tried to edit, rename, and change the ligand type still there is an error.
> Ans in few residues it is showing as torsional marginal outliers errors.
>
>
>
> Please look at the attached screenshot. Please assist me with this.
>
> Best,
> Jeevan.
>