RE: AMBER: problem with group input and NMR restaints

From: Ross Walker <>
Date: Tue, 4 Nov 2008 07:46:17 -0800

Hi Priya,

I'm not sure if you can use NMR restraints with harmonic restraints, I have never tried it although I don't see why it wouldn't work. With regards to your input I think the group input has to come last. so your input should probably be:

Stage 1
  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,
 &wt type= 'REST', istep1 =0, istep2=0, value1=1.0, value2=1.0, /
 &wt type='END' /
hold the protein fixed
ATOM 1 900

Although you may have to experiment here to be sure.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Fri Dec 05 2008 - 10:41:57 PST
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