RE: psfgen problem, not generating angles/dihedrals

From: JC Gumbart (
Date: Sat Sep 11 2010 - 07:10:02 CDT

Try adding this line to your topology file:


I think that should work. Alternatively, the line "regenerate angles dihedrals" after the coordpdb command in psfgen should accomplish the same thing.

-----Original Message-----
From: [] On Behalf Of Rajan Vatassery
Sent: Saturday, September 11, 2010 1:25 AM
To: JC Gumbart
Subject: RE: namd-l: psfgen problem, not generating angles/dihedrals

        Thanks, that does solve the coordinate problem, but I'm still having
problems with the connectivity. There are no angles or dihedrals being
defined by psfgen. I assume that the fix is as simple as the previous
one, but I am stuck. I will give it another go tomorrow, but if someone
sees the problem before then, I am all ears.


On Fri, 2010-09-10 at 23:43 -0500, JC Gumbart wrote:
> 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
> To:
> 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:
> and
> 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

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