AMBER Archive (2007)

Subject: Re: AMBER: minimization not running

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Mar 29 2007 - 04:15:36 CST

Hi,

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 ...

cheers
vlad

deepti nayar wrote:

> hi
>
> I am trying to minimize a dipeptide of phenylalanine-
> dehydrophenylalanine. but it shows the following error.
>
> [root_at_Bic11 exe]# sander -O -i min.in -o phe_delphe.min.out -c
> newdelphe.x -p delprmtop -r phe_delphe.min.x
>
> Unit 10 Error on OPEN: refc
>
>
> my min.in file is attacht here.
>
> i have specified the required torsions in RST file.
>
>
> kindly tell me where i am going wrong.
>
>
>
> thanks
> deepti 

-- 
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Dr. Vlad Cojocaru

EML Research gGmbH
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69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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