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AMBER Archive (2003)Subject: AMBER: SHAKE poblem with dummy atoms
From: Itziar Maestre Asenjo (itziar_at_qorws1.uab.es)
Dear Amber users
I would like to perform a FEP calculation to study the difference in
I have to make the perturbation between a H and a CH3 group, so I have
I have already build the topology file with the 3 dummies (using leap),
My input file looks like
TBBNALA Escalfament
imin = 0, nmropt = 1,
ntx = 1, irest = 0, ntrx = 1,
ntf = 2, ntb = 0, dielc = 1.0,
ibelly = 0, ntr = 0,
maxcyc = 500, ncyc = 5000, ntmin = 1,
nstlim = 10000, t = 0.0, dt = 0.001,
temp0 = 298.0, tempi = 0.0,
ntp = 0, pres0 = 1.0, comp = 44.6,
ntc = 2, tol = 0.00005,
&end
&wt
&rst
&rst
and in the lasts lines in the output file are:
Coordinate resetting (SHAKE) cannot be accomplished,
Note: This is usually a symptom of some deeper
Can anybody help me in understanding the problem there is in this
Thank you very much in advance
Itziar
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