RE: Autopsf error with a modified top file

From: CHINDEA Vlad (vchindea_at_hotmail.com)
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

Vlad
 
> Date: Thu, 19 Feb 2009 19:52:52 -0600
> From: petefred_at_ks.uiuc.edu
> To: vchindea_at_hotmail.com
> CC: namd-l_at_ks.uiuc.edu
> 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
>
>
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