AMBER Archive (2005)

Subject: Re: AMBER: Error on restrained MD equilibration (AMBER 7)

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Tue May 31 2005 - 10:52:48 CDT

L Jin wrote:

>Dear Amber users,
>
>I am running a MD equilibration to heat up the system from 0 to 300K while
>restrained the solute weakly with the following input file. But there is an
>error message about decoding the variable in the input file, which seems to be
>something related to the variable 'ntr = 1'. If I changed 'ntr = 1' to 'ntr =
>0' the output was OK but that would not restrain the solute. Could anybody
>indicate any mistake I have made? Many thanks
>..
> &wt
> type='END',
> &end
>Group input for restraint atoms
> 10
>RES 1
>END
>END
>
try specifying the selection of restrained residues as a range, i.e.
RES 1 1 (instead of RES 1)

Also, if you're using amber8, you can use restraint_wt=10 and
restraintmask=':1' variables in your &cntrl section instead of an older
group input. Oh, I only noticed now (in your subject line) that you're
using amber7...

Cheers,
-Viktor
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