AMBER Archive (2003)

Subject: Re: AMBER: Freezing the residues

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Fri Oct 10 2003 - 14:25:04 CDT

Hello,

Here's where DAC would say:
tell us what you actually did (not just what your intentions were) ...
:)
So IF the input file that you used for restrained minimization is the
one below then you need to add ntr = 1 and use a refc file.

While it is accepted that force constants should be small
(~ single digit) for dynamics, force constants can be ~3 orders
of magnitude bigger for minimizations. Still I have read
recommendations to decrease 4 digit force constants for minimizations.
A google search on
force constant ntr site:structbio.vanderbilt.edu
gets many hits. The tutorials also have info and examples on this.

Scott

On Fri, 10 Oct 2003 zhaoxc_at_puccini.che.pitt.edu wrote:

> 2 is too small, you should try 500 or something.
>
> On 10 Oct 2003, Vikas Varshney wrote:
>
> 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 :
> >
> >A restart file is written every NSTLIM steps for both
> >dynamics and minimization.
> >
> > > -----Original Message-----
> > > From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> > > Of Vikas Varshney
> > > Sent: Thursday, October 09, 2003 5:40 PM
> > > 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
> > >
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