RE: psfgen problem, not generating angles/dihedrals

From: JC Gumbart (
Date: Fri Sep 10 2010 - 23:43:20 CDT

You forgot the line

coordpdb 3tPhAcid-082010.pdb TTH

after the segment command.

-----Original Message-----
From: [] On Behalf Of Rajan Vatassery
Sent: Friday, September 10, 2010 11:34 PM
Subject: namd-l: psfgen problem, not generating angles/dihedrals

Dear List,
        I have been trying to get a new molecule minimized via NAMD and I am
still stuck on the syntax of the required files. I have a molecule that
I will attempt to replicate many times around the surface of a sphere,
but so far I can't get to the minimization of even one molecule. My
problem is with psfgen. I can load psfgen fine, and since I'm debugging,
I'm using it line-by-line. Here is the output:


vatasser_at_mirror15 [~/ClassicalMech] % psfgen
PSFGEN from NAMD 2.6 for Linux-amd64
% topology 3tPhAcid-082010.rtf
reading topology file 3tPhAcid-082010.rtf

% segment TTH {pdb 3tPhAcid-082010.pdb}
building segment TTH
reading residues from pdb file 3tPhAcid-082010.pdb
extracted 1 residues from pdb file
Info: generating structure...
Info: segment complete.
% writepdb TerthiophenePSFGEN.pdb
Info: writing pdb file TerthiophenePSFGEN.pdb
Info: pdb file complete.
% writepsf TerthiophenePSFGEN.psf
Info: writing psf file TerthiophenePSFGEN.psf
total of 59 atoms
total of 62 bonds
total of 0 angles
total of 0 dihedrals
total of 0 impropers
total of 0 cross-terms
Info: psf file complete.


the two files that I have set as input above are here:
PDB File:
RTF File:

The problem is that there are no angles or dihedrals included in the psf
file that psfgen creates. An additional, but less significant problem is
that all the xyz coords in the new pdb file are 0,0,0 and it also
appears that psfgen is reordering the names of the atoms.

Here are the output files from the above instance of psfgen:

Basically, I just want to be able to minimize a molecule that doesn't
already have a defined pdb file and psf file. Any way that I can do that
would be great, but it is likely that I'll need NAMD's parallel
capabilities as my system gets bigger.

Thanks a lot for the help,


Rajan Vatassery

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