From: John Stone (
Date: Fri Dec 10 2004 - 02:22:22 CST

  The solvate plugin doesn't directly generate Parm files for Amber,
(it currently emits a PSF/PDB combination), but it should be possible
to generate the structure as PSF/PDB, load it into VMD, then have VMD
write out the same structure as an Amber Parm file. The main question
is whether that will work or if you'll have to change atom names/types
etc to match what Amber wants. I'm definitely not an Amber expert, so I
can't say whether this will work cleanly or not, but it's certainly
worth a quick try with a simple structure if you have a few minutes to
experiment. I suspect there will be a "gotcha" to fix, but we might
be able to script something to make this easier if it isn't as simple
as straighforward structure file translation.


On Fri, Dec 10, 2004 at 10:34:12AM +0800, wrote:
> Can the solvate plugin of VMD add water moleculars in the amber crd/parm files?
> Kai
> --
> USTC Alumni Email System

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:                 Phone: 217-244-3349              
  WWW:      Fax: 217-244-6078