AMBER Archive (2006)

Subject: Re: AMBER: MD with restraint (nmropt=1)

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Wed Dec 06 2006 - 23:14:56 CST

> Sorry that I did not give enough information. Here is the error message,
> input and DISANGE files I used.
...
> The input file is as follows:
> Initial minimisation of our complex
> &cntrl
> imin=1, maxcyc=500, ncyc=200, ntr=0,
> cut=16, ntb=0, igb=1, nmropt=1
> &end

In general, you need a terminating comma, "," after each variable...

> &wt type = "END"&end
> DISANG=./DISANG.rst

Then, sometimes the namelists are particular in that there should be a
space before the specification, i.e.

 &rst

instead of

&rst

(sometimes with the other variables indented further).

With NMROPT=1 specified, then you need comma's after each variable...

> # distance restraints
> &rst iat=-1, iresid=1, 4
> IALTD=1
> r2=2.0, r3=5.0, r4=10.0
> igr1 = 1,4
> GRNAM1(1)=O4
> GRNAM1(4)=H61
> &end

 &rst iat=-1, iresid=1,4, ialtd=1,
    r2=2.0, r3=5.0, r4=10.0,
    igr1 = 1,4,
    GRNAM1(1)=O4,
    GRNAM1(4)=H61,
 &end

This is assuming that the specification above is correct...

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