Dear AMBER users,
I am attempting to move from an explicit solvent protocol (working, but slow) to
the GB simulations for large, multi-chain RNA structures (~260-300nt, with a diameter
in excess of 120A), using Amber10 (sander.MPI).
I adapted a multi-step protocol, starting with minimization, and
following with five steps; first heating to 300K and four MD runs with diminishing
constraints applied to all the nucleotides (holding at 2.0, 1.0, 0.5. 0.1), all adding up
to 500ps of simulation time. The minimized and equilibrated structures are very similar,
and don't raise any concerns upon examination. However, within the first few hundred
steps of the production MD run, the whole structure inflates rapidly, the helices flatten
(unwind) and the chains barely hold together (for igb=1) or fall apart (igb=2).
The production MD run results indicate some fundamental problems with the input
parameters I am using, but I don't see what is wrong (samples appended below)
after comparing them to the GB tutorials I found on the web. One difference is ntx=5,
instead of ntx=1 (tutorials); another is use of Berendsen, rather than Langevin
thermostats.
I would appreciate comments/corrections on the parameters used, and general comments
on the applicability of the GB method to large RNA molecules.
Best regards, Voytek Kasprzak
1. LeAP script input
source leaprc.ff99bsc0
set default PBradii mbondi
mol-loadpdb file.pdb
saveAmberParm mol file-amb.prmtop file-amb.inpcrd
savepdb mol file-amb.pbd
quit
2. Minimization input:
&cntrl
imin=1, ntx=1, drms=0.01,
irest=0, ntxo=1,
cut=999,
ntpr=100, ntwx=100, ntwe=100,
nsnb=20,
maxcyc=20000, ncyc=1000,
igb=1, saltcon=1.0, ntt=0, offset=0.13,
gbsa=1, ntb=0,
&end
3. Heating
&cntrl
imin=0, ntx=1,
irest=0, ntxo=1,
cut=999, tempi=0.0,
ntpr=500, ntwx=500, ntwe=500,
nstlim=100000, tautp=0.5, temp0=300.0,
dt=0.001, nscm=100,
igb=1,ntb=0, saltcon=0.5, gbsa=1,
ntt=1, nsnb=20, offset=0.13, ntr=1,
&end
GROUP FOR CONSTRAINTS
20.0
RES 1 264
END
END
4. MD with constraints (last of 4 phases shown):
&cntrl
imin=0, ntx=5,
irest=1, ntxo=1,
cut=999, tempi=300.0,
ntpr=1000, ntwx=1000, ntwe=1000,
nstlim=100000, tautp=2, temp0=300.0,
dt=0.001, nscm=100,
igb=1, ntb=0, saltcon=0.5, gbsa=1,
ntt=1, nsnb=20, offset=0.13, ntr=1,
&end
GROUP FOR CONSTRAINTS
0.1
RES 1 264
END
END
5. MD input (things go awry v. quickly)
MD-RUN GBSA production run with Berendsen thermostat (ntt=1)
&cntrl
imin=0,ntx=5,
irest=1, ntxo=1,
igb=1, cut=999, gbsa=1, ntb=0, saltcon=0.5,
ntt=1, temp0=300.0, tempi=300.0,
nscm=100,
nstlim=1000000,
dt=0.001, nscm=100,
ntwprt=0,
ntpr=1000, ntwx=1000, ntwe=1000,
nsnb=20, offset=0.13, tautp=2,
ig=-1,
&end
&wt
type='END'
&end
Wojciech (Voytek) Kasprzak [Contractor]
Analyst Programmer,
Basic Science Program, SAIC-Frederick, Inc.
National Cancer Institute in Frederick, Frederick, MD
(301) 846 5537
www-lecb.ncifcrf.gov/~kasprzak
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Received on Thu Sep 22 2011 - 09:30:03 PDT
