AMBER Archive (2005)

Subject: Re: AMBER: rst file problems

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Mon Apr 11 2005 - 22:13:21 CDT

Dear simmerling,

Thanks for your help.
Yes, my system contains crystallographic waters which
fly off into large distances as the temperature
increases from 0K to 300K. Even when the temperature
is fixed at 300K the water molecules fly off. How can
I deal with this problem. Should I impose some
restraints on the water molecules? If so how can I do
that.
thanking you,

--- Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>
wrote:
> 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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===========================================================================

/\/\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

===========================================================================

________________________________________________________________________
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