VMD-L Mailing List

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Mon Dec 01 2008 - 14:16:48 CST

as far as I know,
vmd/psfgen can not write the prmtop file for amber.

eddi

On Dec 1, 2008, at 1:52 PM, oguz gurbulak wrote:

> Hi Dear VMD Users,
>
> I'm now trying to prepare initial structure ( a pdb file ) and get
> the prmtop and inpcrd input files for MD simulation in AMBER9
> program package. I want to do MD simulations for 500 octane
> molecules and position molecules in defined regions of space in a
> cubic simulation box. Can I do it and create a pdb file with using
> VMD ? If it is possible , I would be very grateful if you can help
> me to learn this operation. I waiting for the contributions.
>
> Thank you very much for your attention.
>
> Kind regards
>
>

=====================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
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