VMD-L Mailing List

From: Sinclair, Matt (mts7_at_illinois.edu)
Date: Sun Jul 30 2023 - 13:03:28 CDT

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.