VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 13 2010 - 11:39:50 CDT

Aaron,
  If you query the atom type fields using a regular atom
selection, do they return the correct values in VMD itself?
It appears to me that the ILS plugin code is just doing a
VMD atom selection query to get the list of types, and
so they may have been truncated when they were originally
read in. Did you read them in from a PSF file?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jul 10, 2010 at 11:25:38AM +1000, Aaron Oakley wrote:
> Hi all,
>
> I want to do an ILS calculation that requires two parameter files:
> -par_all27_prot_na.prm
> -par_all36_cgenff.prm
>
> The calculation wont run and gives the followig errors:
> Warning) Could not find parameters for atom type CG2R
> Warning) Could not find parameters for atom type CG33
> Warning) Could not find parameters for atom type HGR6
> Warning) Could not find parameters for atom type NG2R
> Warning) Could not find parameters for atom type OG2D
> Warning) Could not find parameters for atom type OG31
>
> These are the atoms in the ligand. It appears that the script is
> reading only the 1st 4 characters of the atom types. They should
> be CG2R62, CG331 etc.
>
> Any help appreciated.
>
> thanks,
>
>
>
> A/Prof Aaron Oakley
> School of Chemistry
> University of Wollongong
> Northfields Avenue
> Wollongong, NSW, 2522
> Australia
> Phone: (02) 4221 4347
> Fax: (02) 4221 4287
> Email: aarono_at_uow.edu.au
> 

-- 
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