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
&rst
iat=-1,-1,
IRESID=0,ir6=0,
r1=50.0, r2=55.0, r3=55.0, r4=60.0, rk2=10.0, rk3=10.0,
igr1=5,15,32,48, ............1686,
igr2=1732,..........,3133,3152,
/
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
Angstroms
(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,
rk3=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
