tmao molecule

From: Vasudevan V (
Date: Wed May 20 2009 - 09:43:40 CDT


I am a new user of namd and I am trying to create a tmao molecule. I did the
following steps but nothing gets written into my psf and i do not get any
explicit error message also. My pdb contains exactly one molecule of tmao
with Hydrogen atoms explicitly definied.

I added the following definition to the topology

RESI TMA 0.000 !
ATOM N1 NTL 0.440
ATOM O2 NO -0.650
ATOM C3 CTL3 -0.260
ATOM C4 CTL3 -0.260
ATOM C5 CTL3 -0.260
ATOM H6 HAL3 0.110
ATOM H7 HAL3 0.110
ATOM H8 HAL3 0.110
ATOM H9 HAL3 0.110
ATOM H10 HAL3 0.110
ATOM H11 HAL3 0.110
ATOM H12 HAL3 0.110
ATOM H13 HAL3 0.110
ATOM H14 HAL3 0.110
BOND N1 O2 N1 C3 N1 C4 N1 C5
BOND C3 H6 C3 H7 C3 H8
BOND C4 H9 C4 H10 C4 H11
BOND C5 H12 C5 H13 C5 H14

and I have defined the bond and angle parameters for the NO bond in the
parameter file.

NO NTL 347.564 1.4070 ! TMAO Nitrogen Oxygen

and the pgn file i use to generate is as follows

package require psfgen
topology top_tmao.inp
coordpdb tmao_namd.pdb
writepdb tma.pdb
writepsf tma.psf

but there are no atoms being written into the psf file which i generate. The
output of the script is

Info) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)
Info) Email questions and bug reports to
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 2 CPUs detected.
Info) Free system memory: 3450MB (88%)
reading topology file top_tmao.inp

>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>> 410-706-7442 or email: alex, <<<<<<<<<
  \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
  \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
              Alexander D. MacKerell Jr.
                     August 1999
 All comments to ADM jr. email: alex,
              telephone: 410-706-7442

Created by CHARMM version 27 1
Info: writing pdb file tma.pdb
Info: pdb file complete.
Info: writing psf file tma.psf
total of 0 atoms
total of 0 bonds
total of 0 angles
total of 0 dihedrals
total of 0 impropers
total of 0 cross-terms
Info: psf file complete.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:50 CST