Dear amber user,
I am a new user of amber. I am facing one difficulty in SMD simulation.
I have a protein compelx consisting of proteins gp120 and cd4.
I want to separate them using SMD. The pulling force is applied between
center of mass of two proteins. The criteria for pulling is that the
center of mass of gp120 will be fixed and the center of mass of cd4 will
move.
Following are my input files
md_pull.in
ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
ntpr = 500, ntwx = 500, ntwv = 0, ntwe = 0,
ntwprt = 0, ntwr = 500,
ntf = 2, ntb = 1, dielc = 1.0,
cut = 9.0, nsnb = 10,
scnb = 2.0, scee = 1.2,
ipol = 0, ibelly = 0, ntr = 1,
imin = 0,
maxcyc = 500,
ncyc = 2000,
ntmin = 1, dx0 = 0.1, dxm = 0.5, drms = 0.0001,
nstlim = 50000, nscm = 1000,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 300.0,
ig = 71277, heat = 0.0,
ntt = 1, dtemp = 0.0,
tautp = 1.0,
vlimit = 20.0,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 0.5,
ntc = 2, tol = 0.0005,
jar = 1
&end
Hold cm of gp120 fixed
10000.0
ATOM 1714
END
END
&wt type='DUMPFREQ', istep1=1 /
&wt type='END' /
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
END
END
--------------------------------------------------------------------------
dist.RST
&rst iat=1714,6932, r2=40.9,r2a=75.0, rk2=50.0 /
Can someone please tell me where should I change in input parameter to
make atom 1714 fix .
Thanking you in advance.
Bidisha
Indian Institute of Science, Bangalore
India
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Received on Wed May 20 2009 - 12:55:30 PDT
