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
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