Hi Amber Users,
Thanks Scott and Asim for answering my query. I got restrt file now.
I want to freeze some of my residues during 'minimization'. What should I do. I tried
to use RES in input file for sanders with force constant value 2 but the atom moved a
lot after the minimzation. Should I use higher value of force constant like 100 or am I
missing something. I will appreciate if you can answer my queries.
Thanks & regards,
VIkas Varshney
Dept. of polymer science
University of Akron.
On Fri, 10 Oct 2003 Scott Brozell wrote :
>Hello,
>
>ntwr applies to dynamics not minimization.
>A restart file is written every NSTLIM steps for both
>dynamics and minimization.
>
>When I tried your input, after decreasing the surprisingly large
>maxcyc to 700, using the prmtop and inpcrd from test/ubiquitin,
>a restart file was written at step 700.
>Without knowing the details of your system it is recommended
>that maxcyc be reduced by a couple of orders of magnitude.
>
>Scott
>
>On Thu, 9 Oct 2003, Asim Okur wrote:
>
> > To be able to write a restrt file you have to use ntwr in the input
> > file.
> >
> > ntwr = 10
> >
> > will write to the restart file every 10 steps,
> >
> > Asim Okur
> >
> >
> >
> > -----Original Message-----
> > From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> > Of Vikas Varshney
> > Sent: Thursday, October 09, 2003 5:40 PM
> > To: amber.scripps.edu
> > Subject: AMBER: Not getting restrt file on running sanders
> >
> > Dear AMBER users,
> > I tried to run minimization of a system of around 500 residues (~5000
> > atoms) in
> > sander with option -r restart, but did not get the restart file. Here is
> > my input file.
> > Minimization
> > &cntrl
> > imin=1,maxcyc=100000,ntmin=2,
> > ntpr=10,iwrap=1,
> > &end
> > Group input for restrained atoms
> > 2.0
> > RES 383 478
> > END
> > END
> >
> > I will really appreciate if you are can help me with this.
> >
> > Many regards and thanks,
> >
> > VIkas Varshney
> > Dept. of polymer science
> > University of Akron.
> >
> >
> > <http://clients.rediff.com/signature/track_sig.asp>
> >
>
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Received on Fri Oct 10 2003 - 04:53:02 PDT
