VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Feb 12 2010 - 22:58:35 CST

The commands you listed are really random. Why would you reset the psf
immediately before trying to write it? Or require the package psfgen after
you use it?

I would suggest looking at the example in the NAMD tutorial for building a
psf. Then everything should become clear.

The error about atom C comes about because the topology file you are using
tries to apply NTER and CTER patches by default (it thinks everything is a
protein). You can circumvent this by including the lines "first none" and
"last none" inside your segment command.

Also, you have a typo in your pdb; OS2 is listed twice.

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Ronald Salesky
Sent: Friday, February 12, 2010 7:41 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: psfgen generates 0 atom .psf file

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,

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