AMBER Archive (2006)

Subject: Re: AMBER: REMD: Hybrid topology file

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
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.
carlos

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
>ala3.sol.top.strip in the rem_hybrid test directory does not.
>So, is there a particular way of generating this hybrid parmtop file?
>Thanks,
>austin-
>
>PS. Standard REMD works with parmtop files generated in AMBER8
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu