psfgen fails to set coords for all atoms

From: Blake Mertz (
Date: Fri Nov 27 2009 - 15:06:47 CST

I'm running into a problem with my setup for MD testing of a molecule
fragment against some QM results that I've compiled. My situation is this:
I've got my fragment and want to do a dihedral scan of a methyl group. The
appropriate fixed atoms are prepped with their values in the occupancy
field, and all of my atoms are in the intial positions I want them, so I
really don't need psfgen to guess their coordinates. I've spent the last
couple weeks trying to find some answers on namd-l, but haven't really run
across anyone with the specific error "Warning: failed to set coordinate"
for every atom in their molecule. Here are some short examples from my
files, starting with the psfgen output:

reading topology file

>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
 All comments to ADM jr. via the CHARMM web site:
               parameter set discussion forum

Created by CHARMM version 31 1
cross-term entries present in topology definitions
reading topology file

 retinal/retinol and related model compounds

Created by CHARMM version 32 1
aliasing residue UNK to RTC5
building segment C5
disabling angle autogeneration
disabling dihedral autogeneration
reading residues from pdb file C5-p10-vmd.pdb
extracted 1 residues from pdb file
Info: generating structure...
Info: segment complete.
reading coordinates from pdb file C5-p10-vmd.pdb for segment C5
Warning: failed to set coordinate for atom CT UNK:1 C5
Warning: failed to set coordinate for atom CT2 UNK:1 C5
Warning: failed to set coordinate for atom CT2 UNK:1 C5
Warning: failed to set coordinate for atom CT2 UNK:1 C5
Info: guessing coordinates for 36 atoms (14 non-hydrogen)
Warning: failed to guess coordinates for 36 atoms

My pdb file was generated in vmd, but here are the first few lines:
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 CT UNK X 1 -0.621 0.576 -2.166 1.00
ATOM 2 CT2 UNK X 1 -1.811 0.043 -2.987 1.00
ATOM 3 CT2 UNK X 1 -3.104 0.006 -2.177 1.00

My topology file, which was modeled after Jan Saam's for retinal:
!read rtf card append
* retinal/retinol and related model compounds
32 1

RESI RTC5 0.00 ! retinal C5-methyl fragment,
                     ! nomenclature from PDB based on retinol
ATOM C1 CT 0.00
ATOM C2 CT2 -0.18
ATOM H21 HA 0.09

My pgn file:
package require psfgen
topology /home/blake/Documents/NAMD/toppar/top_all22_prot_cmap.inp
pdbalias residue UNK RTC5
segment C5 {
  auto none
  pdb C5-p10-vmd.pdb
coordpdb C5-p10-vmd.pdb C5
writepdb test.pdb
writepsf test.psf

And output test.pdb:
REMARK original generated coordinate pdb file
ATOM 1 C1 RTC5X 1 0.000 0.000 0.000 -1.00 0.00 C5
ATOM 2 C2 RTC5X 1 0.000 0.000 0.000 -1.00 0.00 C5
ATOM 3 H21 RTC5X 1 0.000 0.000 0.000 -1.00 0.00 C5
ATOM 4 H22 RTC5X 1 0.000 0.000 0.000 -1.00 0.00 C5

Sorry for the long email, I just haven't been able to find any good answers
to this so far, and am getting frustrated trying to figure it out myself.
Any help is definitely appreciated.

Blake Mertz

Research Assistant
Department of Chemistry
University of Arizona
"Life is not easy for any of us. But what of that? We must have perseverance
and above all confidence in ourselves. We must believe that we are gifted
for something and that this thing must be attained." Marie Curie
"Start by doing what's necessary; then do what's possible; and suddenly you
are doing the impossible." St. Francis of Assissi

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