AMBER Archive (2004)

Subject: Re: AMBER: RE:sander8

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Oct 12 2004 - 06:21:02 CDT

Vincent,
it isn't clear waht you mean by the angles "were the same". Were they
supposed to change from the initial values (were the restraint values
different from the initial ones)? If so, look at the sander output to
make sure it actually read the restraints ok, and also look at the
restraint energy, which should be high at the beginning (if input crd
and restraint target values do not match) and then it should go down.
Carlos

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

Vincent Bisetty wrote:

>Dear Carlos,
>Thanks for your suggestions- it finally worked. After minimization, I
>used ambpdb to generate my pdb files-and the measured torsion angles
>were the same. Heres my 2 input files ( min.in and rst.f).
>Now I am looking for a dihedral angle driver for amber8. Any
>suggestions..
>regards, vincent.
>
>min.in
>...
>minimization
> &cntrl
> imin=1, maxcyc=5000, ncyc=5000, ntmin=1,
> drms=0.001, dielc=1,
> ntx = 1, dt=0.002, nmropt=1,
> ntb=0, cut=10.0, temp0= 200, tempI=200,
>/
> &wt type='END' /
> LISTOUT=POUT
> DISANG=rst.f
>..........
>
>rst.f
>.....
> &rst iat= 5,7,9,32, r1=-210, r2=-180, r3=-180,
> r4=-150, rk2=50, rk3=50, /
>
> &rst iat=7,9,32,34, r1=-210, r2=-180, r3=-180,
> r4=-150, rk2=50, rk3=50, /
> &rst iat=0
>/
>
>
>Dr K Bisetty
>Senior Lecturer
>Department of Chemistry
>Steve Biko Campus
>Durban Institute of Technology
>P O BOX 1334
>Durban
>4000
>Tel : +27-031-2042311
>Fax : +27-031-2022671
>"ND-4-SPD"
>bisettyk_at_dit.ac.za
>
>
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