AMBER Archive (2006)

Subject: Re: AMBER: MD with positional and NMR restraints

From: Mike Summers (summers_at_hhmi.umbc.edu)
Date: Thu Dec 07 2006 - 17:34:07 CST

Thanks David. I thought I had tried that before, but apparenly I
had left off the comma after the 'END' statement.
It's working great now.

Mike

 On Thu, Dec 07, 2006 at 01:51:53PM -0800, David A. Case wrote:
> On Thu, Dec 07, 2006, Mike Summers wrote:
>
> >
> > Is there any way to use both positional and NOE restraints? The script
> > shown in (C) below runs but does not implement the NOE restraints.
> >
> >
> > (C) (Doesn't apply the NMR restraints.. permutations I've tried also don't work) ############
> >
> > &cntrl
> > nmropt=1,
> > imin=0,
> > irest=0,
> > ntx=1,
> > ntb=0,
> > cut=10,
> > ntc=2,
> > ntf=2,
> > tempi=0.0,
> > temp0=300.0,
> > ntt=3,
> > gamma_ln=1.0,
> > nstlim=10000, dt=0.002,
> > ntpr=100, ntwx=100, ntwr=1000
> > ntr=1,
> > /
> >
> > &wt type='END' /
> > keep main chain atoms frozen
> > 500.0
> > FIND
> > * * M *
> > SEARCH
> > RES 20 145
> > END
> > END
> >
> > &wt type='END' /
> > LISTOUT=POUT
> > DISANG=../RST.dist
> > /
> > eof
> >
>
> The trick is to try to follow exactly the table at the top of p. 89 of the
> Amber Users' Manual (version 9; the equivalent info is pretty well hidden in
> version 8). According to that, here is what should work:
>
> title goes here <-- "title"
> &cntrl <-- cntrl namelist
> nmropt=1,
> imin=0,
> irest=0,
>
> ....
>
> ntr=1,
> /
> &wt type='END', / <-- varying conditions
> LISTOUT=POUT <-- file redirection
> DISANG=../RST.dist
> <-- end of file redirection cards
> keep main chain atoms frozen <-- group information
> 500.0 <-- see note below
> FIND
> * * M *
> SEARCH
> RES 20 145
> END
> END
>
>
> I ran this on a test case, and it seemed to work fine.
>
> [A note: 500 is a very large force constant for the restraints. A value
> 10-50 times smaller will serve to effectively keep the backbone fixed (say to
> within 0.1 Ang.) while giving much less opportunity for dynamics problems to
> arise because of the strong constraints.]
>
> Please let me know if you still have problems!
>
> ...regards....dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

-- 

*********************************
Michael F. Summers
Department of Chemistry and Biochemistry
  and Howard Hughes Medical Institute
University of Maryland Baltimore County
1000 Hilltop Circle 
Baltimore, MD 21250

Phone: (410)-455-2527  
FAX:   (410)-455-1174
Email: summers_at_hhmi.umbc.edu
Web:   www.hhmi.umbc.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu