Re: [AMBER] Creating distaint restaint in Amber

From: David A Case <case.biomaps.rutgers.edu>
Date: Thu, 10 Mar 2011 08:56:18 -0500

On Thu, Mar 10, 2011, Vivien Landre wrote:
>
> I want to create one restrain between the C1 of the C-terminal glycine
> in one molecule and the nitrogen in the lysine group of another
> molecule. I want the restrain to be between 1.2 and 2. I have already
> looked through previous entries in the mailing list and as far I as I
> understand I have to create lines in the restraint file specifying the
> restraint looking like this:
>
> # 34 LYS NZ 183 GLY C 1.2 2
> &rst
> ixpk= 0, nxpk= 0, iat= 586, 2969, r1= 0.7, r2= 1.2, r3= 2, r4=2.5,
> rk2=25.o, rk3=25.0, ir6=1, ialtd=0,
> &end #
>
> ? I want to create the restrain between atom 586 (34 LYS, NZ) and atom
> 2969 (183 GLY C).
>
> However I am not sure how and where to insert the lines in the .rst
> file?

They go in a separate file, and the name of that file is given on the DISANG
card in the main mdin file. Also, set nmropt=1 in the &cntrl namelist. See
examples in Section 6.11 of the Users' Manual.

...good luck...dac


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Received on Thu Mar 10 2011 - 06:00:06 PST
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