[AMBER] restraints on group of atoms

From: Dhananjay <dhananjay.c.joshi.gmail.com>
Date: Mon, 14 Dec 2015 17:47:47 +0800

Dear users,

I could successfully run the MD with restraints on C-alpha atoms of two
chins (A and B) of a protein. I used following "disang" files specifier to
apply restrains on centre of geometry of CA atoms.

Disrance restraint
  r1=50.0, r2=55.0, r3=55.0, r4=60.0, rk2=10.0, rk3=10.0,
  igr1=5,15,32,48, ............1686,

I want to keep the two chins at certain distance limit such that the centre
of geometry (CoG) distance difference will be between 50.0 to 60.0
(i.e., I want 50.0 <= [CoG(chainA)-CoG(chianB)] <= 60.0 )

To achieve this, I specify: r1=50.0, r2=55.0, r3=55.0, r4=60.0, rk2=10.0,

I am getting partial success:
Though the chin A and B do not exceed 60.0 angstroms, i.e. upper limit,
however, quite often fall close with distance less than 50.0 angstroms
(~30.0 Ang.).

Did I missed something here ? Any suggestions please !!

I am using Amber 14 with pmemd.cuda version on GPU with all latest updates.

Thanking you in advance.

-- DJ
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Received on Mon Dec 14 2015 - 02:00:05 PST
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