[AMBER] Restrained MD with COM restraint with PMEMD

From: Mike Limb <mikeallimb.gmail.com>
Date: Tue, 3 Dec 2013 22:16:59 +0000

Dear AMBER users,

I trying to run some restrained Molecular dynamics on GPUs using pmemd.

In each of these MD simulations I fix the ligand in position using a COM
restraint that is specified in rc.con

# COM restraint with NAM-D and CD of Glu35 (between 1 and 6 A)

&rst
r1=-500,r2=1.0,r3=6.0,r4=500,
rk2=50,rk3=50,
iresid=1,
iat=130,35,
ATNAM(1)='C1','C2','C3','C4','C5','O5',
ATNAM(2)='CD',
/

Although the calculations runs using sander, I have found that they do not
run using pmemd.

pmemd -O -i md_10ns.i -o md_0-10.out -p boat2.prmtop -c eq_all_npt.rst -r
md_10ps.rst -x test.mdcrd &

(where md_10ns.i is attached)

They crashing immediately with the error message:

forrtl: severe (18): too many values for NAMELIST variable, unit 33, file
/work/bristol/eisbr037/AMBER/HEWL/restrained/1cons_loose/boat2/rc.con, line
8, position 33

(indicating an issue with the syntax in rc.con, the same syntax that works
for sander)

I know that certain functionality is not supported in pmemd, but looking in
the manual it doesn't say these restraints aren't possible so I am a bit
confused why it doesn't work.

Any help would be most welcome,

M

-- 
Mike Limb
PhD Candidate
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Supervisor: Prof. Adrian Mulholland
Centre for Computational Chemistry
School of Chemistry
University of Bristol
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Bristol BS8 1TS
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at UoB
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Received on Tue Dec 03 2013 - 14:30:02 PST
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