VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 26 2007 - 15:50:55 CDT

Hi,
  You'll need to perform the same slicing and dicing on the main
structure file as you've done on the DCD, so that you can load the
DCD with the new structure to view the simulation. Since you're working
with AMBER inputs, you may find it easiest to do this by using
atom selections to chop the same portions of the structure you chopped
using catdcd, and writing it out to a new PDB/PSF pair. Once you've
got those, then you can load the PDB, PSF, and DCD into VMD and everything
should work fine. The PSF generated by this operation won't be useful
for simulation since it will have lost the angles/dihedrals/impropers etc,
but it will preserve the same bonding information that was in your original
AMBER data, but for the selected subset of atoms.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 26, 2007 at 09:08:44AM -1000, Irene Newhouse wrote:
>
> I've simulated a fairly large system & would like to look at only a particular region, so I did a web search & was able to find out how to write an index file to use in catdcd, to select only the portion of interest. Now I'm stuck a simpler problem - what files do I load into VMD to let me animate the resultant file? I had a web page at one point which might have helped, but I lost the URL & try as I might, can't recover it.
>
> Incidentally: I'm using AMBER inputs, as the ligand to my protein is a saccharide for which there aren't good CHARMM parameters, while there's GLYCAM for AMBER, which has a literature base behind it.
>
> Thanks!
> Irene Newhouse
> _________________________________________________________________
> Windows Live Hotmail and Microsoft Office Outlook – together at last.  Get it now.
> http://office.microsoft.com/en-us/outlook/HA102225181033.aspx?pid=CL100626971033 

-- 
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