AMBER Archive (2009)

Subject: Re: [AMBER] Is it the way to do simulation in vacuum

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Oct 30 2009 - 05:21:49 CDT

we need to see your sander input.
also- what does your sander run script look like? if you do a "top" on that
machine, is sander still running?

Dear community,
> I am trying to simulate my protein in vacuum. I am
> preparing the topology and parameter files as follows
>
> $ tleap
> > source leaprc.ff99SB
> > mol=loadpdb pdb
> > saveamberparm mol prmtop inpcrd
> >quit
>
> Then I have run the minimization of 250 cycles. But this small minimization
> is not coming out. And investigating the output file by "tail -f" command
> only shows the following
> --------------------------------------------
> AMBER 9 SANDER 2006
> --------------------------------------------
>
> I am unable to find the defect in the procedure. Please help.
>
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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