RE: Autopsf error with a modified top file

From: CHINDEA Vlad (
Date: Fri Feb 20 2009 - 19:28:28 CST

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

> 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!

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