Re: AMBER: minimization not running

From: Vlad Cojocaru <>
Date: Thu, 29 Mar 2007 12:15:36 +0200


If I am not wrong your input is not appropiate for reading NMR-like
restraints. NTR=1 is for positional restaints and not for NMR-like
restraints. If you set NTR to 1, sander will try reading and refc file
that you normally specify with -ref flag when running sander (see
manual). ANd since you dont define a refc file, your minimization crashes...

For NMR-like restraints you should first have NMROPT set to 1 ... You
should check the manual ... for instance at page 199 you have a sander
sample input for simulated annealing using NMR-like restraints ... You
could adapt that input for a simple minimization ...


deepti nayar wrote:

> hi
> I am trying to minimize a dipeptide of phenylalanine-
> dehydrophenylalanine. but it shows the following error.
> [root.Bic11 exe]# sander -O -i -o phe_delphe.min.out -c
> newdelphe.x -p delprmtop -r phe_delphe.min.x
> Unit 10 Error on OPEN: refc
> my file is attacht here.
> i have specified the required torsions in RST file.
> kindly tell me where i am going wrong.
> thanks
> deepti

Dr. Vlad Cojocaru
EML Research gGmbH
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Received on Sun Apr 01 2007 - 06:07:24 PDT
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