Re: [AMBER] Dummy atom and PMEMD

From: Jason Swails <>
Date: Thu, 30 Aug 2012 16:05:11 -0400

On Thu, Aug 30, 2012 at 3:21 PM, Ali M. Naserian-Nik

> Dear Jason,
> Thank you for reply. I have added the non-bonded dummy atoms to the
> topology file and do some SMD simulations vi sander without any problems.

How did you add them?

> Nevertheless, the problem is with pmemd. Does the way you suggested for
> adding the dummy atom enable pmemd to support simulations with the dummy
> atoms?

What are the error messages? pmemd has better error checking on the whole
than sander does, so if something is running with sander but not pmemd due
to changes in the topology file, my guess is something is wrong and you
don't know it.

My suggestions should work in pmemd, but the error messages contain the
best clues.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Aug 30 2012 - 13:30:04 PDT
Custom Search