AMBER Archive (2004)

Subject: Re: AMBER: MD with NTR + NMROPT

From: David A. Case (case_at_scripps.edu)
Date: Mon May 10 2004 - 10:46:06 CDT

On Mon, May 10, 2004, Martin Fabani wrote:

> Hi, I'm trying to perform a short MD in AMBER7 and I
> would like to know if it is possible to do such simulation
> holding a part of my structure fixed (ntr=1) and including
> NMR distance restraints (nmropt=1) for another part of
> the structure, at the same time.
> The typical protocol I used is:
> &cntrl
> igb = 1,
> ntb = 0,
> ntp = 0,
> ntt = 1,
> temp0 = 300.0,
> tempi = 0.0,
> nstlim = 20000,
> dt = 0.001,
> ntwx = 500,
> ntwv = 500,
> ntpr = 500,
> ntwe = 500,
> imin = 0,
> cut = 99.0,
> ntr = 1,
> nmropt = 1,
> saltcon = 0.2,
> gbsa = 1,
> &end
> Group input for restrained atoms
> 5.0
> RES 3 42
> END
> END
> &wt type = 'END'
> &end
> DISANG = phn.disang
> END

As the manual states on p. 91, "the restrained atoms are read in GROUP format
after all other input..." So, put the GROUP input _after_ the "DISANG ="
line.

...good luck...dac

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