AMBER Archive (2008)

Subject: Re: AMBER: NMR refinement

From: David A. Case (
Date: Fri Jan 18 2008 - 11:11:54 CST

On Thu, Jan 17, 2008, Wenyong Tong wrote:
> Here is my result of annealing with NMR refinement. Could you please give me
> some suggestions about this ?

Not clear what sort of suggestions you are looking for...

> &cntrl
> ntwx=500, ntpr=500, ntwe=500, ntwv=500,
> ntt=1, temp0=1000.0, tempi=5.0,
> igb=1, saltcon=0.05, offset=0.13,
> scnb=2.0, scee=1.2, dielc=80, cut=100.0,
                       this is ignored (I hope!) See the manual. It
                       certainly safer not to use it
> ntb=0, ntc=2, ntf=2,
> nstlim=100000, dt=0.0020,
> vlimit=10, rgbmax=30.0,
> ntp=0,
> ibelly=0, ntr=0,
> imin=0, irest=0, ntx=1, nmropt=1,


> NMR restraints: Bond = 196.802 Angle = 0.000 Torsion = 0.000

You still have some energy in the NMR restraints. Set LISTOUT=POUT to examine
these in detail. The "sviol" (summarize violations) script might also be
worth running to help examine where the remaining violations are.


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