Hello All,
Some additional information regarding to my previous post, here is the
input file I used for the production runs:
MD simulation
&cntrl
imin = 0, nstlim = 25000000 , irest = 1, ntx = 5, dt = 0.002 ,
ntt = 3, temp0 = 300.0, gamma_ln = 2.0, ig = -1,
ntc = 2, ntf = 2, cut = 10.0 , ntwprt=7586 ,
ntb = 2, ntp = 1, pres0 = 1.0, taup = 1.0, barostat=2,
ioutfm = 1, iwrap = 1, nmropt=1,
ntwx = 5000, ntpr = 5000, ntwr = 50000 ,
/
&ewald
/
&wt type = 'END'
/
&rst
iat=130,7570, r1=1.0, r2=1.5, r3=3.2, r4=3.8,
rk2=5.0, rk3=5.0,
/
.
. some more distance restraints
.
I suspect that Amber does not write out the restart file properly, or
the restart runs were not dealt with properly. Could some one please
have a check for me? It really bothers me. Thanks a lot!
All the best,
Qinghua
-------- Forwarded Message --------
Subject: simulations of enzyme with ligand
Date: Thu, 16 Nov 2017 17:51:19 +0100
From: Qinghua Liao <scorpio.liao.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Hello,
I did some simulations of an enzyme in complex with a ligand, the
complex sits in a octahedral box with water molecules.
I applied some distance restraints between the ligand and the enzyme in
order to keep the ligand stable at the binding site,
the force constant was set as 5 kcal/mol A2.
However, I found that there are some snapshots that the ligand goes out
of the binding site. I thought that it could be
the PBC problem, but I still got the long distance between the ligand
and the enzyme after I did the correction with autoimage.
I then check the output file, I found the restraints energy was
extremely high than the other frames.
Here are the distances calculated using cpptraj with autoimage
correction (only one of four is present):
# frames distance (angstrom)
14999 3.1086
15000 2.8088
15001 52.0178
15002 14.3344
15003 3.4264
15004 3.0565
And here are the restraints from the output file:
# frames Restraints (kcal/mol)
14999 0.0350
15000 0.4185
15001 1209.4373
15002 294.3320
15003 20.4252
15004 20.2892
As I did the production runs step by step, each step is for 50 ns (5000
frames). It means that the jumping-out happened
at the first frame of step 4 (frame 15001). I then checked the last
frame of step 3 ( frame 15000) from the restart file,
I found that the ligand was out of the binding site, and the restart
file which was not done with PBC correction (the ligand is still out of the
enzyme) was used for the the next step simulation. I did the simulations
with iwrap=1 and ioutfm=1.
Any comment and suggestion? Thanks a lot!
All the best,
Qinghua
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Received on Sun Nov 19 2017 - 07:30:03 PST
