Re: Autopsf error with a modified top file

From: Peter Freddolino (
Date: Fri Feb 20 2009 - 23:19:22 CST

Hi Vlad,
psfgen must have residue names in order to build a psf; otherwise, how
is it supposed to know what residue a given collection of atoms is
supposed to be? You should be ok without the other fields, so long as
autopsf split the chains properly. You will need to be exceedingly
careful to keep your columns aligned properly as you add in the residue
name; please be sure to consult the pdb file format reference available


CHINDEA Vlad wrote:
> Hi Peter
> I have tried as suggested but except for the fact that IMPR, CMAP and IC
> warnings are missing now, everything else is the same. When I try to do
> the same with a pgn script in TKCon I get a different kind of messages:
> "
> reading coordinates from pdb file xxx for segment Y
> no residue of segment Y
> Warning: Failed to set the coordinates for atom OH
> no residue of segment Y
> .
> "
> and so on for every atom in the molecule.
> Could this be related to the fact that in the PDB I have blank residue
> name, residue ID, segment name and line number columns ?
> I have attached the PDB for your reference.
> Kind regards and all the best
> Vlad
>> Date: Thu, 19 Feb 2009 19:52:52 -0600
>> From:
>> To:
>> CC:
>> Subject: Re: namd-l: Autopsf error with a modified top file
>> Hi Vlad,
>> your topology file actually includes *empty* IMPR, CMAP, and IC
>> statements, which is syntatically invalid. Try deleting them and see if
>> things work.
>> Best,
>> Peter
> ------------------------------------------------------------------------
> Invite your mail contacts to join your friends list with Windows Live
> Spaces. It's easy! Try it!
> <>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:23 CST