Hello. I am trying to set up a umbrella sampling simulation in order
to calculate the free energy associated with the separation of two
transmembrane alpha helices. I have tried to modify the sample file
given in the amber manual in order to change from an angle restraint
into a distance restraint, using as reference points the COM of both
helices.
Here is the md.in file:
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 3, csurften = 3, gamma_ten = 17,
ninterface = 2 taup = 2.0,
cut = 8.0,
ntr = 0,
ntc = 2,
ntf = 2,
temp0 = 310.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 500000, dt = 0.002,
ntpr = 1000, ntwx = 1000, ntwr = 10000,
ig = -1, ioutfm = 1, iwrap = 1
nmropt=1,
/
&wt type='DUMPFREQ', istep1=10 /
&wt type='END' /
DISANG='dist.RST'
DUMPAVE=dist_vs_t.11
And the dist.RST file I have used
&rst restraint = "distance(com(1-33.N,CA,C) com(34-66.N,CA,C)), r1=0.,
r2=11., r3=11., r4=35.0, rk2 = 30., rk3 = 30.,
I am trying to run pmemd.cuda. Once type the command pmemd.cuda...etc,
I get the following error on the mdout file.
Warning: Error opening "Old" file from subroutine OPNMRG
File = 'dist.RST'
Does this mean that the syntax I have used for the dist.RST file is
wrong? If so, how would I prepare such simulation?
Thank you
Fabrício
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Received on Mon Sep 17 2012 - 13:30:02 PDT
