Hi, I am experimenting a TI perturbation with Amber 8.0 on an
enzyme-catalyzed bimolecular reaction (an alcohol reacts with a
carboxylic acid to form an ester). The two species are away from each
other in the enzyme pocket. First I run the simulation in vaccum
without enzyme. I defined two new atom types for the carbonyl carbon
(CX) and the hydroxyl oxygen (OX). They will become C and OS at the
end (in the ester) and one OH and two HO atoms will disappear.
Initially CX and OX distance is 6.0 angstrom. When I run minimization
on the unperturbed system, the 1-4 EEL blows up quickly. I suspect
that this has something to do with the restraints between two
molecules. I tried to play around the force constants and so far has
no luck. Any suggestions will be welcomed.
Eric
Initial minimisation of our complex
&cntrl
imin=1, maxcyc=2500, ncyc=1000,
cut=1000,ntb=0, ntpr=50
/
....
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -8.6624E+01 6.0486E+00 3.0066E+01 C4 4
BOND = 2.9020 ANGLE = 40.9876 DIHED = 28.3713
VDWAALS = -3.3408 EEL = 58.0670 HBOND = 0.0000
1-4 VDW = 12.8320 1-4 EEL = -226.4433 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
150 -5.6925E+03 6.0827E+04 4.8485E+05 H15 15
BOND = 6.7995 ANGLE = 78.2618 DIHED = 38.3658
VDWAALS = -2.9570 EEL = 54.6162 HBOND = 0.0000
1-4 VDW = 12.2254 1-4 EEL = -5879.7886 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -1.1864E+07 2.6376E+11 2.1022E+12 H15 15
BOND = 6.6603 ANGLE = 78.2334 DIHED = 38.3939
VDWAALS = -2.9575 EEL = 54.6011 HBOND = 0.0000
1-4 VDW = 12.2257 1-4 EEL = ************* RESTRAINT = 0.0000
emark goes here
MASS
CX 12.010 0.616 same as c
OX 16.000 0.434 same as o
BOND
CX-OX 10.0 6.0 weak restraint
ANGLE
CX-OX-CT 10.0 117.18
CX-OX-HO 10.0 117.18
O -CX-OH 10.0 120.00 same as O -C -OH
O -CX-OX 10.0 120.00 same as O -C -OH
OH-CX-OX 10.0 117.18
CA-CX-OX 10.0 120.00 same as CA-C -OH
DIHE
X -CA-CX-X 4 14.50 180.0 2. same as X -C -C -X
X -CT-OX-X 3 0.50 0.0 3. same as X -CT-OH-X
X -CX-OH-X 2 4.60 180.0 2. same as X -C -OH-X
X -CX-OX-X 2 4.60 180.0 2. same as X -C -OH-X
IMPROPER
NONBON
CX 1.9080 0.0860 same as c
OX 1.6612 0.2100 same as o
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Received on Wed Apr 06 2005 - 18:53:00 PDT
