Date: Fri, 23 Oct 2015 12:56:31 +0100
Hi AMBER users,
I am trying to simulate a reaction involving the formation of a covalent
bond using umbrella sampling combine with QM treatment of the reaction
atoms. I have the SG atom of a cysteine residue attacking an electrophilc
carbon on a ligand. The distance between these 2 atoms is the reaction
coordinate. The windows of umbrella sampling are spaced 0.3 Angstrom apart.
The restraint file looks like this:
#
# 123 CYM SG 432 UNK C1 3.43
&rst
ixpk= 0, nxpk= 0, iat=1937,6803, r1= 2.93, r2= 3.43, r3= 3.43, r4= 3.93,
rk2=0.0, rk3=100.0, ir6=1, ialtd=0,
&end
and the md.in file looks like this:
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2,
cut = 12,
ntr = 0,
ntc = 1,
ntf = 1,
igb = 0
ntp = 1
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim =10000, dt = 0.001
ntpr = 1000, ntwx = 1000, ntwr = 1000, nmropt = 1,
ifqnt=1,
/
&qmmm
qmmask =
'.1934-1937,6794-6848',
qmcharge =
0,
qm_theory =
'PM3',
qmcut =
12.0,
/
&wt type='DUMPFREQ', istep1=100,/
&wt type='END' /
DISANG=RST-1.dist
LISTOUT=POUT
DUMPAVE=DIST_1.dat
The run was able to simulate the formation of the bond at the end and the
next graph represents the values of the coordinates across the windows.
[image: Inline images 1]
Is that sufficient overlap? If it is not, do I need to reduce the spacing
or increase the force constant to get better overlap?
I used the WHAM code by Alan Grossfieldto calculate PMF with this command:
wham 1.59 3.73 70 0.00001 300 0 meta.dat result.dat
and this was the meta.dat file:
DIST_1.dat 3.43 200
DIST_2.dat 3.13 200
DIST_3.dat 2.83 200
DIST_4.dat 2.53 200
DIST_5.dat 2.23 200
DIST_5.dat 1.93 200
DIST_7.dat 1.63 200
and the histogram I am getting looks like:
[image: Inline images 2]
I was expecting the histogram to look different, the PMF to go higher and
then decreases as it approcahes the products. If I managed to improve the
overlapping, will this change the histogrm?
Many thanks,
Mahmood Jasim
Aston University
UK
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(image/png attachment: image.png)
(image/png attachment: 02-image.png)
