Dear all
I am working on DNA-ligand system. I generate force field parameter by
antechamber. At first I do two stage minimizations then two step
equilibration, and finally 10 ns MD production (inputs is attached). I am
facing a problem when visualizing trajectory with VMD, one of the
terminal basepairs is jumped out of the box, the covalent bond which
attached ligand to two adjacent nucleotides, is broken up, and the
separated ligand made bad interact with other nucleotides. As a result DNA
helix begins to deformation.
I tried to image the ligand back into the box by ptraj, resulting
no improvement in trajectory visualization. Extracting one snap out of the
trajectory shows that the ligand is completely separated from DNA, and
located in improper position out of box and helix is completely opened. But
RMSD plot shows good shape which fluctuate around 4 angstrom.
My question is:
How can I perform MD for my complex to retain the covalent bonds between
DNA and ligand?
Is it OK, if I use position restraint on DNA around production time ( to
make DNA structure more stable)?
The input files is listed below:
*min1*
&cntrl
imin = 1,
maxcyc = 5000,
ncyc = 2500,
ntb = 1,
ntr = 1,
cut = 10.0
/
Hold the DNA fixed
500.0
RES 1 77
END
END
*min2*
&cntrl
imin = 1,
maxcyc = 5000,
ncyc = 2500,
ntb = 1,
ntr = 0,
cut = 10.0
/
*eq*
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2,
ig =-1,
pres0 = 1.0,
ntp = 1,
taup = 2.0,
cut = 10.0,
ntr = 0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 100000,
dt = 0.002,
ntpr = 200,
ntwx = 200,
ntwr = 1000
/
*10 ns md*
&cntrl
imin =0,
irest =1,
ntx =5,
nstlim=5000000,
dt =0.002,
ntc =2,
ntf =2,
cut =10.0,
ntb =2,
ig =-1,
ntp =1,
taup =2.0,
ntpr =1000,
ntwx =1000,
ntt =3,
gamma_ln=2.0,
temp0 =300.0,
/
Any help is appreciated.
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Received on Wed Oct 29 2014 - 04:00:02 PDT
