In my first mail I have mistyped. I am having problem with the substrate
molecule simulation. The receptor simulations are going fine.
We have derived the atomic charges for the substrate molecule using RESP,
and then fed to AMBER8, explicit method ff99 force field.
The following is the equilibration protocol
sub_min1.in
MMB4: initial minimization solvent + ions
&cntrl
imin = 1,
maxcyc = 1000,
ncyc = 500,
ntb = 1,
ntr = 1,
cut = 12.0
/
Hold the MMB4 fixed
500.0
RES 1 1
END
END
sub_min2.in
MMB4: initial minimization of whole system
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 1000,
ntb = 1,
ntr = 0,
cut = 12.0
/
Then I have heated the system for 100ps
sub_md1.in
MMB4: 100ps MD with protein on MMB4
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 8.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 15.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 50000
dt = 0.002
ntpr = 500, ntwx = 500, ntwr = 1000
/
keep MMB4 fixed with weak restraints
10.0
RES 1 1
END
END
sub_md2.in
then equilibration was done for 900 ps
MMB4: 900ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 8.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 450000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 1000
/
sub_md3.in
then under NVT conditions the system was equilibrated for 10 ns
MMB4: 1000ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 1,
cut = 8.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 500000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 1000
/
After the equilibration process I have started performing TI calculations,
at first I made all the atomic charges zero on the substrate molecule, then
ran the simulations for 2 ns and equilibrated for 1ns, each for 8 clambda
values at klambda=6. These calculations were done successfully. Now I am
running the TI calculations to make the vanderwaals forces zero, and at the
clambda =.129, the rst file got corrupted. For all the TI calculations the
following input file
neturalize MMB4
&cntrl
ntr=0, nstlim = 1000000,
ntave = 1000, nscm = 10000,
ntx =7, irest =1, ntpr = 1000, ntb =1,
dt =0.001, nrespa =2,
ntt =3, gamma_ln = 1.0, tempi = 300, temp0 = 300,
ntc = 2, ntf = 2, tol = 0.00001,
ntwr = 1000, ntwx =1000,
icfe = 1, clambda = 0.12923, klambda = 6
/
Finally I have to yet the analyze the GMAX trend in the caluclations.
manikanthan
> _______________________________________________
>
--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 12 2010 - 16:30:03 PDT
