AMBER Archive (2006)

Subject: Re: AMBER: REMD: Hybrid topology file

From: Carlos Simmerling (
Date: Wed Aug 30 2006 - 09:48:20 CDT

I have not used a rdparm prmtop for hybrid calculations, that
may be the problem. Try making a prmtop in leap without a box
and see if it helps. If not, send me your prmtop directly and I'll
see if I can track down the problem.

Austin B. Yongye wrote:

>Dear AMBER users,
>I tried to do a hybrid REMD in AMBER9, but got this error message:
> "GB/PB calculations now require a new-style prmtop file"
>The full topology file was created by LEAP in AMBER8.
>The entire system has 670 water molecules. But I would like to keep only
>100 for energy calculation during replica exchange.
>The hybrid parmtop file, was generated using the stripwater option in
>rdparm. The bottom of my hybrid parmtop file has box information, but the
> in the rem_hybrid test directory does not.
>So, is there a particular way of generating this hybrid parmtop file?
>PS. Standard REMD works with parmtop files generated in AMBER8
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to