Try changing it from iat(3) in your call to just iat=-1,-1,r1=...
I don't believe iat(3) is part of the namelist.
-Charlie
________________________________________
From: Dhananjay (達南杰) [d00b46022.ntu.edu.tw]
Sent: Thursday, December 03, 2015 6:56 AM
To: amber.ambermd.org
Subject: [AMBER] pmemd.cuda with CoM restraints
Dear users,
I successfully run the MD with restraints applied on two atoms (in cpu) using disangle specifier as follows:
#Disrance restraint
&rst
iat=1220,18, r1=0.0, r2=50.0, r3=50.0, r4=55.0, rk2=10.0, rk3=10.0,
/
Now, I wish to extend this to protein and a peptide system and want to keep them at certain distance by applying distance restraints on centre of mass/geometry of two groups of atoms. Therefore, I used igr1 and igr2 as follows:
#Disrance restraint
&rst
iat(3)=-1,-1, r1=0.0, r2=15.0, r3=15.0, r4=20.0, rk2=10.0, rk3=10.0,
IRESID=1,
igr1=1,2,3,4,5,6,7,8,9,10,
igr2=123,124,125,126,127,128,129,130,131,132,133,134,135,136,
/
I used pmemd.cuda(GPU) and got following error:
CUDA (GPU): Implementation does not currently support the use of COM simulations for angle or dihedral restraints.
Require iat(3) >= 0.
I do not want to apply angle or dihedral restraints but distance only.
What is wrong here ?
Any help in this regard will be appreciated !!
Thanks in advance,
-- Joshi
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Received on Thu Dec 03 2015 - 09:30:02 PST
