Re: AW: "Warning" meaning

From: Salvatore Mario Cosseddu (S.M.Cosseddu_at_warwick.ac.uk)
Date: Fri Mar 02 2012 - 04:53:19 CST

The pair was generated using vmd 1.8 (and the included psfgen).

I don't know why this strange behaviour.

I rebuilt the system from scratch using vmd 1.9. Many thanks.

Regards
Salvatore

On 02/03/12 07:03, Norman Geist wrote:
>
> 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 <mailto: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 <mailto: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 <mailto:S.M.Cosseddu_at_warwick.ac.uk>

-- 
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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