AMBER Archive (2004)

Subject: Re: AMBER: MD simulations with 2 molecules

From: David A. Case (
Date: Wed Feb 18 2004 - 16:15:04 CST

On Wed, Feb 18, 2004, Joey Harriman wrote:
> I am trying to do a MD simulation with two molecules. However, when I try
> to load both prep files (prepi) it resets the coordinates.

It's not clear exactly what you tried, or what happened. The general
procedure for setting up two molecules that are not bonded to each other
is to prepare a prei file for each of them, and a pdb file with the starting
coordinates. Put a TER card between the two molecules, then use loadPdb
to get things set up in leap.

> In addition I have had problems using the prepc format for prep files.

Not much anyone can do to help with messages like this. You have to say
what you tried and what happened; be as specific as you can.



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to