VMD-L Mailing List

From: José Villalaín (jvillalain_at_umh.es)
Date: Thu Feb 11 2021 - 08:23:50 CST

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