VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Dec 01 2012 - 22:32:47 CST

Hi,
  STRIDE (the program that VMD uses to determine secondary structure)
most likely doesn't recognize the residue names (and/or atom names, etc) in
your structure file, so it is unable to compute the secondary structure.
You can fix this by using conventional (e.g. matching the PDB) names.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 30, 2012 at 11:49:23PM -0800, Shubhadip Das wrote:
> Dear VMD-L User,
>
> I have a pdb file of a protein which has residue name "MOL" for each
> residue. When I tried to load its graphical representation in cartoon
> option the following lines appears in window.Will you please let me know
> how should I proceed to avoid this problem.
>
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 147
> Info) Bonds: 150
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 1
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 1 Protein: 0 Nucleic: 0
> Info) In any publication of scientific results based in part or
> Info) completely on the use of the program STRIDE, please reference:
> Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
> Info) assignment. Proteins: structure, function and genetics, 23,
> 566-579.
> Error reading PDB file /tmp/fileLRrl7d
> ERROR) Unable to find Stride output file: /tmp/fileoIA3rD
> ERROR) Stride::read_stride_record: unable to read output file from Stride
> ERROR) Call to Stride program failed.
> Info) VMD for LINUX, version 1.9.1 (February 1, 2012)
> Info) Exiting normally.
>
> Thanking you in advance
> Sincerely,
> Shubhadip Das
> Research Scholar
> IIT Guwahati
> India 

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