AMBER Archive (2006)

Subject: Re: AMBER: multiple "restraint_wt" in sander

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Mon Jul 03 2006 - 09:43:44 CDT

Dear Takanori,

with the new (from Amber8 on) "restraintmask" syntax, there's no way to
specify different restraint weights. You may still be able to use old
GROUP input at the end of your input file which allowed different
weights for different regions. However, this feature may disappear in
future amber releases in favor of "restraintmask" which simplifies input
file structure...

Cheers,
-Viktor

kanazta1_at_yahoo.co.jp wrote:
> Dear AMBER community,
> Just a quick question.
> It it possible to specify different restraint weights for different
> parts of a protein?
> There is no complaint from sander for an input something like
> --------------------------------------------
> ntr=1, restraint_wt=10.0, restraint_mask=':1-10',
> restraint_wt=1.0 , restraint_mask=':11-20'
> --------------------------------------------
> but, it appears that only the last restraint was accepted.
> A search in the archive gave a similar question, but there was no
> reply there.
> Many thanks in advance,
> Takanori
>
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-- 
===================================================================
Viktor Hornak
Center for Structural Biology   Phone: (631)632-1439
SUNY at Stony Brook             Fax:   (631)632-1555
Stony Brook, NY 11794-5115      E-mail: viktor.hornak_at_sunysb.edu
=================================================================== 

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