Hi,
I am minimization a protein complex where I have decided to keep all the
crystal waters - this might be one of my problems though. I want to start a
minimization of the crystal water
Minimization of water molecules rest is fixed
&cntrl
imin = 1,
maxcyc = 50000,
ncyc = 25000,
ntb = 0,
ntr = 1,
igb = 0,
cut = 12
/
Hold protein fixed
500.0
RES 1 802
END
END
The first of the minimization the energies explode which I presume are due
to bad vdw interaction -clashing I have tried to change the dt=0.00001 but
that did not solve the problem. I would prefer not to remove too many of the
crystal waters but could I try just to minimize the hydrogens in the system?
I have tried selection like
ATOM '!.H'
instead of RES but this is a wrong syntax how to fix this?
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Received on Thu Jul 22 2010 - 06:30:04 PDT
