AMBER Archive (2006)

Subject: AMBER: REMD: Hybrid topology file

From: Austin B. Yongye (
Date: Wed Aug 30 2006 - 09:30:34 CDT

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
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