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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Received on Fri Dec 05 2008 - 10:41:28 PST
