From: Axel Kohlmeyer (
Date: Fri Feb 12 2010 - 22:52:25 CST


if you call resetpsf right before you wrie the psf file, it will be empty.
also you have to tell psfgen, that it should not try to add any terminating
patches. it by default assumes, that you want to builda peptide topology.


On Fri, Feb 12, 2010 at 8:41 PM, Ronald Salesky <> wrote:
> Hello fellow VMD users,
> I am attempting to generate a .psf file for the SDS surfactant. A .pdb file
> (attached below) was preparced using coordinates from Pubchem and the atom
> names used were those in describing the residue SDS in the topology file
> top_all27_prot_lipid_na.inp by hand in a text editor. When using psfgen from
> the Tkconsole, the resulting .psf file has 0 atoms, 0 bonds, etc. (This is
> similar to my result using autopsf which gives a warning that an atom must
> be selected.) It's probably an obvious thing to experienced users, but can
> anyone suggest where I'm going wrong? (the tkconsole commands are listed
> below along w/ the sds.pdb file attached.)
> Much thanks,
> Ron
> -----------------
> mol load pdb sds.pdb
> topology plugins/.../top_all27_prot_lipid_na.inp
> segment SDS {
> pdb sds.pdb
> }
> package require psfgen
> resetpsf
> writepsf SDS
> -----------------------------
> Note the response to segment SDS { pdb sds.pdb } was
> building segment SDS
> reading residues from pdb file sds.pdb
> extracted 1 residues from pdb file
> Info: generating structure...
> no atom C in residue SDS:1 of segment SDS <<this is odd, many carbon atoms
> in SDS
> Warning: add conformation failed in patch NTER
> Info: segment complete

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.