From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Wed Aug 24 2011 - 18:05:18 CDT
I do not know how to do it with namd or vmd, however, alternatively you may open the output pdb file with Chimera software ( http://plato.cgl.ucsf.edu/chimera/ ) and just save it as pdb. Chimera defaults will change ATOM records from any ligands to HETATM, as well change the atom names based on a default PDB topology dictionary.
I hope it helps.
--- On Wed, 8/24/11, hamze rahimi <buksanbio_at_gmail.com> wrote:
From: hamze rahimi <buksanbio_at_gmail.com>
Subject: namd-l: convert pdb format to normal pdb format
To: "vmd-l" <vmd-l_at_ks.uiuc.edu>, namd-l_at_ks.uiuc.edu
Date: Wednesday, August 24, 2011, 10:48 AM
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:44 CST