From: Ronald Salesky (
Date: Fri Feb 12 2010 - 19:41:10 CST

Hello fellow VMD users,

I am attempting to generate a .psf file for the SDS
surfactant. A .pdb file (attached below) was prepared
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,


mol load pdb sds.pdb
topology plugins/.../top_all27_prot_lipid_na.inp
segment SDS {
pdb sds.pdb
package require psfgen
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

  • application/vnd.palm attachment: sds.pdb