Dear Amber users
I would like to perform a FEP calculation to study the difference in
energy between a receptor and the two enantiomers of a N-acetyl-alanine.
I have to make the perturbation between a H and a CH3 group, so I have
to add 3 dummies atoms on the H.
I have already build the topology file with the 3 dummies (using leap),
and I have also minimzed the structure.
Now I am trying to perform a MD simulation, with the aim of obtaining a
stable structure, and begin the FEP simulation with this structure, but
I am finding SHAKE problems in performing the MD simulation.
My input file looks like
TBBNALA Escalfament
&cntrl
imin = 0, nmropt = 1,
ntx = 1, irest = 0, ntrx = 1,
ntxo = 1, ntpr = 1000,
ntwx = 1000, ntwv = 0, ntwe = 1000,
ioutfm = 0, ntwprt = 0, ntwr = 500,
ntf = 2, ntb = 0, dielc = 1.0,
cut = 9.0, nsnb = 10,
scnb = 2.0, scee = 1.2, ipol = 0,
ibelly = 0, ntr = 0,
maxcyc = 500, ncyc = 5000, ntmin = 1,
dx0 = 0.1, dxm = 0.5, drms = 0.0001,
nstlim = 10000, t = 0.0, dt = 0.001,
temp0 = 298.0, tempi = 0.0,
ig = 71277, heat = 0.0,
ntt = 1, dtemp = 0.0,
tautp = 0.5, vlimit = 20.0,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 0.5, npscal = 1,
ntc = 2, tol = 0.00005,
&end
&wt
type='END'
&end
&rst
iat=10,117 r1=3.0, r2=5.0, r3=15.0, r4=17.0,
rk2=10., rk3=10.0,
&end
&rst
iat=30,125 r1=3.0, r2=5.0, r3=15.0, r4=17.0,
rk2=10., rk3=10.0,
&end
and in the lasts lines in the output file are:
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 3 57 130 131
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Can anybody help me in understanding the problem there is in this
simulation?
And has anybody any suggestion to solve this problem?
Thank you very much in advance
Itziar
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Received on Tue Sep 09 2003 - 12:53:02 PDT
