From: David Hardy (
Date: Thu Feb 11 2021 - 08:49:53 CST

Dear Jose,

Recent version of NAMD do have support for lone pairs. Can you explain more about the problems you are having with lone pair support in NAMD? Also, if this becomes a NAMD support issue, we could move the conversation to the namd-l list.

Best regards,

David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801,
> On Feb 11, 2021, at 8:23 AM, José Villalaín <> wrote:
> Dear all,
> I have been trying to build a small organic molecule having a chloro group (to obtain the psf and pdb files, along with the topology and parameter files) using CGenFF (Charmm-Gui web server, using both PDB_Reader and Ligand_Reader). The problem is that the chloro group is acompanied by a lone pair and the molecule is not supported by NAMD in that format. I have been trying to change both the pdb and psf files with no success until now.
> Would it be possible to change the pdb/psf files to delete the lone pair so that NAMD runs smoothly?.
> Thanks a lot.
> José
> Prof. José Villalaín
> Department of Biochemistry and Molecular Biology
> Univesitas Miguel Hernández, Alicante, Spain