Dear Amber users,
I am trying to simulate a double stranded RNA but when I run the code
no .rst file is created which I need for further simulation. (This is
the fourteenth simulation run, there are 21.)
equilibration
&cntrl
nstlim=50000, cut=12.0, ntr=1,
ntpr=500, ntwr=10000, ntt=1, ntwx=5000, temp0=300.0, tempi =300.0,
ntx=5, irest=1, scnb=2.0, scee=1.2,
ntc=2, ntf=2, tol=0.00005,
dt=0.002, ntb=0,tautp=2.0,
nscm=500,
igb=5, gbsa=1, saltcon=0.2,
intdiel=1.0, extdiel=78.5,
nrespa=4
/
Keep RNA except terminal ends fixed with weak restraints
80.0
RES 2 21
RES 24 43
END
Keep Terminal ends fixed with weak restraints
100.0
RES 1
RES 22 23
RES 44
END
END
I will appreciate if anyone can offer some suggestions.
I am new to amber so please look for any basic mistakes first as the
chances of committing some novice mistake is more probable.
Abhijeet Chowdhury
Student
M.Sc.(Hons.) Biological Sciences
B.E.(Hons.) Chemical Engineering
Birla Institute of Technology and Science (BITS),
Pilani 333 001, Rajasthan, INDIA
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Received on Wed Apr 06 2016 - 05:30:03 PDT
