AMBER Archive (2002)

Subject: Re: Defining Restraints in Sander

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Thu Jul 18 2002 - 16:29:22 CDT

two comments:

1) the force constant is way too big, it will explode if
they are not at that distance, end even if they are it
will have a very hard time during MD due to the high
frequency. Try 1.0, it should work fine.

2) without the full input file or the output I can't
tell if you told sander to use restraints or not.
please include the entire input and tell us what version
of amber it is. the beginning of the output would
also help.
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant 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
===================================================================

----- Original Message -----
From: "Asif Rahaman" <arahaman_at_chemdept.chem.ou.edu>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Thursday, July 18, 2002 4:21 PM
Subject: Defining Restraints in Sander

>
> I am putting restraint on 2 atoms (2967 and 3295) in the protein at a
> specific distance 6.0558 A with a force constant 950.0 and doing the
> minimization. I define the restraint in the input file in the following
way:
> --------------------------------------------------------------------------
> &end
> &wt TYPE='END'
> &end
> &rst iat=2967,3295,0,0,
> iresid=0, irstyp=0, ifvari=0, imult=0, ir6=0, ifntyp=0,
> nstep1=0, nstep2=0,
> r1=6.0558, r2=9.1, r3=9.1, r4=9.5,
> rk2=950.0, rk3=950.0,
> &end
> &rst iat = 0,0,0,0,
> &end
> ----------------------------------------------
> After the minimization is completed when I view final structure, I found
> that the atoms 2967 and 3295 are not at 6.0588 A away but they are around
> 10 A away.
>
> Could you please let me know if I am doing anything wrong in defining
the
> restraint in the input file. I have looked at the sander manual (amber 5 -
> page 160-163 and page 174). It is confusing to me. Please
help!!!!!!!!!!!!!!
>
> With best regards, Asif
>
>