AMBER Archive (2005)

Subject: Re: AMBER: rst file problems

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Apr 11 2005 - 08:22:41 CDT

you can't just delete data form the restart file, then the
coordinates won't be given to the right atoms.
you need to solve the problem of the asterisks.

it looks like some of your coordinates are larger than
1000 angstroms, while others are much smaller.
did the MD that produced this file complete without
anything unusual, or any large energies?
is the system very large? is it more than 1 molecule? maybe
they have become separated very far in space.
you'll need to look at your system and find out what is
happening to the structure to cause such large
coordinates.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

mathew k varghese wrote:

>Dear amber users,
>I am running a GB simulation of a cyt bulged rna.I
>have run the simulation to 1020ps in 6 steps. the rst
>file written during the 6th step contains some
>asterisk marks and so I could not run the 7th step.
>When I deleated the lines which contains these
>asterisk marks, the sander reports that the velocity
>limit is exceeded for some atoms.The rst file is
>attached and the portion of the rst file is shown
>below. What may be the problem? How can I avoid it?
>
>
>
>302.7039874-184.2375775-360.4247410
>303.7298408-184.1419747-361.4213178
> 371.8875075-134.3744325************
>371.1584642-133.7572813************
> 372.1595619-133.9013809************ 844.9096625
>81.1806288 23.3634199
> 844.0667443 81.3001205 22.8437569 845.4412138
>81.8871922 22.9814963
> -0.9849900 -0.4603898 1.1188423 0.3352386
>0.2888170 0.0935052
> 0.0724099 0.2361661 -0.1595945 -1.1055550
>-0.3351865 -0.7293620
>
>
>===========================================================================
>
>/\/\athew
>
>Mathew K Varghese
>Research Scholar
>School of Pure and Applied Physics
>M.G.University
>Kottayam, Kerala
>India
>
>email mathew_kvarghese_at_yahoo.co.in
>
>===========================================================================
>
>________________________________________________________________________
>Yahoo! India Matrimony: Find your life partner online
>Go to: http://yahoo.shaadi.com/india-matrimony
>

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