Hello Amber Community,
I have several molecules (such as A, B, C, D) and then combine them
together.
The molecules in a file are named as unite A, B, C and D. They have
identical
atoms.
How can i fix or restraint some atoms in molecules A and B?
Is it the good way to use bellymask or restraintmask using atoms number?
Is it the correct format using bellymask with number in sander?
bellymask = .7-21, 28-31, 38-55
I saw somebody mentioned that he tried to use colon, space, ., &, etc. in
between, but
they amber only forzens atoms 7-21 in place:
http://archive.ambermd.org/200907/0175.html
I copied his case as following:
Rigid Backbone Amino Acids& 100ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0, ibelly = 1,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 50000, dt = 0.002,
bellymask =
.7-21&28-31&38-55&62-65&72-75&82-85&92-95&102-117&124-127&134-137&144-147&154-158&165-168&175-178&185-188&195-198&205-213&220-223&230-233&240-244&248-2344,
ntpr = 100, ntwx = 100, ntwr = 1000
/
Thanks a lot for your idea!
Jim
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Received on Tue Feb 09 2010 - 01:00:02 PST
