AW: "Warning" meaning

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Mar 02 2012 - 01:03:10 CST

Hi,

 

usually the tools one use to generate simulation input files shouldn’t
create such funny structures. So it’s good that NAMD is telling you because
this would usually indicate that there (could) has gone something wrong. How
you generated this pdb? Often one uses the resids or atomnumbers as a
reference for various post- and preprocessing, so it’s is not really wanted
that the numbering is not in order as this will make the analysis pretty
complicated.

 

The bottom line is: One should avoid it and look why it happened.

 

Best wishes

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Salvatore Mario Cosseddu
Gesendet: Donnerstag, 1. März 2012 11:27
An: Chris Harrison
Cc: namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: "Warning" meaning

 

Thank you, it's true!

Does this affect NAMD in any way? I read in the source that it creates a new
segment, is it right?
Do you suggest me to manipulate the files?

Regards
Salvatore

On 01/03/12 06:23, Chris Harrison wrote:

Salvatore,

 

It basically means that your psf/pdb pair has a residue possessing a resid
value that is not in consecutive order with the preceeding residue. ie, you
have a list of residues numbered as follows: 79, 80, 82, 81, 83 .... or
something similar.

 

Best,

Chris

 

On Mon, Feb 27, 2012 at 1:55 PM, Cosseddu, Salvatore
<S.M.Cosseddu_at_warwick.ac.uk> wrote:

Dear all,

What does this warning actually mean?

Warning: Residue 81 out of order in segment WAT, lookup for additional
residues in this segment disabled.
Warning: Residue 1 out of order in segment POT, lookup for additional
residues in this segment disabled.
Warning: Ignored 7523 bonds with zero force constants.

Many thanks

--
Salvatore Cosseddu
PhD student
Centre for Scientific Computing and School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom
email: S.M.Cosseddu_at_warwick.ac.uk
 
-- 
Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
http://www.ks.uiuc.edu/Research/namd       Voice: 773-570-6078 
http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
Fax: 217-244-6078
 
 
 
-- 
Salvatore Cosseddu
PhD student
 
Centre for Scientific Computing and School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom
 
email: S.M.Cosseddu_at_warwick.ac.uk

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:16 CST