AMBER Archive (2008)

Subject: AMBER: problem with group input

From: Ed Pate (pate_at_math.wsu.edu)
Date: Mon Jan 21 2008 - 00:53:28 CST

Dear Amber community:

I am trying to do a simulation of a protein-ligand complex in an explicit
box of waters using sander and Amber8. I want to restrain most of the
protein and to have NMR distance restraints on the ligand. My input
parameter file follows:

&cntrl
   imin=0,
   irest=0,
   ntx=1,
   ntt=1,
   temp0=300.0,
   tautp=1.0,
   ntp=1,
   taup=1.0,
   ntf=2,
   ntc=2,
   ntb=2,
   dt=0.002,
   nstlim=1000,
   ntwe=0,
   ntpr=10,
   nmropt=1,
   lastist=30000000,
   lastrst=30000000,
  &end
  &ewald
  &end
  &wt
   type='END',
  &end
LISTOUT=/home/pate/sl2_myosin.d/POUT
DISANG=/home/pate/sl2_myosin.d/RST
   restrain the following
   1.0
RES 1 58
RES 137 207
RES 215 617
RES 636 715
END

The test simulation runs to completion. Checking the md.out file, the
simulation invoked the NMR restraints. However, it did not appear to take
the group input (no statement in the output file about the group residues
and harmonic restraints.)

I would greatly appreciate it if someone could point me in the right
direction for the correct input file.

One other question: It would probably be better to do this simulation
using pmemd (one problem at a time). Would the input file be the same?

Thanks for the help.

Ed Pate

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