[AMBER] Creating distaint restaint in Amber

From: Vivien Landre <V.Landre.sms.ed.ac.uk>
Date: Thu, 10 Mar 2011 03:40:37 +0000

Hello all,

I am new to Amber and have a question regarding setting up a distant
restraint between two residues in two different proteins in Amber.

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? I have created the restraint file, topology and coordinate file
using LEaP.

I would be great if someone could help me with this!

Thanks in advance
Vivien




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Received on Wed Mar 09 2011 - 20:00:02 PST
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