VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 18 2005 - 09:49:33 CST
- Next message: Brian Bennion: "Re: Catching error info before it shuts down ..."
- Previous message: Jérôme Hénin: "Call to Stride program failed"
- In reply to: Jérôme Hénin: "Call to Stride program failed"
- Next in thread: Jérôme Hénin: "Re: Call to Stride program failed"
- Reply: Jérôme Hénin: "Re: Call to Stride program failed"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Jerome,
Stride doesn't like your structure, and is aborting because it couldn't
find any hydrogen bonds. They have a little bit of code that aborts the
secondary structure calculation if it doesn't find H bonds anywhere:
for( Cn=0; Cn<NChain; Cn++ )
PlaceHydrogens(Chain[Cn]);
if( (NHBond = FindHydrogenBonds(Chain,Cn,HBond,Cmd)) == 0 )
die("No hydrogen bonds found in %s\n",Cmd->InputFile);
Are your atom names for your hydrogens unusual for some reason?
John
On Fri, Feb 18, 2005 at 04:42:27PM +0100, Jérôme Hénin wrote:
> Hi all,
>
> When executing a VMD script that performs secondary structure analysis on a
> short peptide, I get this error quite often:
>
> No hydrogen bonds found in /home/henin/tmp/filej1DOme
> ERROR) Unable to find Stride output file: /home/henin/tmp/filegZgQj0
> ERROR) Stride::read_stride_record: unable to read output file from Stride
> ERROR) Call to Stride program failed.
>
> Does anyone know exactly why this is happening?
>
> Thanks,
> Jerome
>
> --
> Jérôme Hénin
> Equipe de Dynamique des Assemblages Membranaires
> Université Henri Poincaré / CNRS
> Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 71
> http://www.edam.uhp-nancy.fr/
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
- Next message: Brian Bennion: "Re: Catching error info before it shuts down ..."
- Previous message: Jérôme Hénin: "Call to Stride program failed"
- In reply to: Jérôme Hénin: "Call to Stride program failed"
- Next in thread: Jérôme Hénin: "Re: Call to Stride program failed"
- Reply: Jérôme Hénin: "Re: Call to Stride program failed"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]