Hi everyone,
I'm absolutely new to Amber and I'm starting to learn how to handle DNA. I
have the following question. This is the code of my simulation:
10-mer DNA MD Generalise Born, 12A cut off
&cntrl
imin = 0, ntb = 0,
igb = 1, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0,
nstlim = 100000, dt = 0.001,
cut = 12, restraint_wt=500.0,
restraintmask=':1,10,11,20',
/
I'm trying to restrain the bases number 1, 10, 11 and 20, but I see in vmd
that they are still moving. What am I doing wrong? I tried to add the
line ntr=1 but that gives me an error "Error opening unit 10: File "refc"
is missing or unreadabl".
Since now thanks a lot!
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Received on Mon Nov 14 2016 - 23:30:03 PST
