Dear Amber user
I am M.Bagherpour an M.Sc student of physics at Institute for Advanced
Studies in Basic Science (www.iasbs.ac.ir).
I am using Amber software for DNA simulation. Specially in my project I
need to fix two ends of DNA strands,The DNA that I want to simulate has 17
sequence.
I have used the two related manual of this package as explain below:
1. "*GROUP commands*":
------
DNA 17-mer: 2ns MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 12.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 1000000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
/
Hold the DNA fixed
10
RES 1
END
Hold the DNA fixed
10
RES 17 18
END
Hold the DNA fixed
10
RES 34
END
END
(Also with fore constant 5 & 20 & 100 & 500)
-----------------------------------------------
2. "*Restraintmask command* " with Restraint_wt=10 and 20 and 50. for 50 is:
----
DNA 17-mer: 10ns MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 12.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
restraint_wt=50.0,
restraintmask=':1,17-18,34',
nstlim = 5000000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
-------------------------------------------
Finally; I found that after about 1ns, these two ends are not fixed and are
separated from each other.
*Now I am wandering if you could advise me a method to fix two ends of DNA
strains.
*
I would appreciate your help.
Looking forward to hearing from you.
Best regards
M.Bagherpour
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Received on Sun Apr 08 2012 - 03:30:04 PDT
