AMBER Archive (2008)

Subject: Re: AMBER: problem with group input and NMR restaints

From: Carlos Simmerling (
Date: Tue Nov 04 2008 - 09:35:46 CST

yes it is possible.
you could try moving the group input to the end of the mdin file. you
might also want to use the "restraintmask" syntax instead of group
input. check the manual for details.
why are you changing "REST" in the weight change section?
be careful that igb=1 is what you really want with a protein- this is
not our "best" GB model for proteins.

On Tue, Nov 4, 2008 at 10:20 AM, priya priya <> wrote:
> 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
> ________________________________
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