VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 04 2009 - 09:49:26 CDT

Hi,
  We don't have a gromacs plugin for reading the .itp or .top files,
so you'd either need to translate your structure into a PSF or some
other bond-specifying file format for which a VMD plugin exists,
or someone would need to write a VMD plugin to read these other gromacs
file types. If someone is interested in writing a VMD plugin for reading
more of the gromacs related files, I would be happy to provide assistance
and help get it going.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 02, 2009 at 05:52:23PM -0400, BAN,YOUNG MIN wrote:
> Hello.
>
> I am trying to represent DPPC lipids as bonds or lines. But since
> I am using Marrink's coarse grained model, it seems that vmd does
> not recognize bonding between coarse grained molecules. I am using
> Gromacs, so I have .gro, .itp, and .top files.
>
> How can the lipids be represented by bonds or lines using those
> .gro, .itp, or .top files? Do I need other type of files to do
> this?
>
> Thanks in advance.
>
> Young-Min Ban 

-- 
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