AMBER Archive (2008)

Subject: AMBER: problem with group input and NMR restaints

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Tue Nov 04 2008 - 09:20:09 CST

Dear Amber community:

 
I am trying to do a simulation of a protein-ligand complex using sander and Amber9. I want to restrain most of the protein and to have NMR distance restraints on the ligand.
After running the simulation and checking the protein_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 out that is it  possible to run MD with harmonic and nmropt restraints at one time.

My input

 
parameter file follows:

Stage 1
 &cntrl
  imin=0, irest=0, ntx=1,
  nstlim=100000, dt=0.002,gbsa =1,surften=0.005,
  ntc=2, ntf=2,ntr=1,
  ntt=3, gamma_ln =5.0,
  tempi=0.000, temp0=300.19,
  ntpr=500, ntwx=500, ntwr = 500,
  ntb=0, igb=1,nmropt=1,
  cut=16
  /
hold the protein fixed
10.0
ATOM 1 900
/
&wt type= 'REST', istep1 =0, istep2=0, value1=1.0, value2=1.0, /
 &wt type='END' /
  DISANG=rst
END

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