Hi all,
I ran tleap on a monomeric protein 1CSQ followed by sander for energy
minimization with distant dependent dielectic constant. The parameters are:
initial minimisation prior to MD
&cntrl
ntpr = 10,
ntb = 0,
igb = 0,
dielc = 4,
cut = 12,
scnb = 2.0, scee = 1.2,
imin = 1, maxcyc =2000,
ncyc=100
&end
&ewald
eedmeth=5,
&end
/
In the end when i studied the output file for the last cycle energy it is:
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 1.8255E+02 1.3963E-01 1.0133E+00 CE2 133
BOND = 17.3608 ANGLE = 79.8825 DIHED =
505.6139
VDWAALS = -508.3373 EEL = -413.0355 HBOND =
0.0000
1-4 VDW = 211.1170 1-4 EEL = 289.9485 RESTRAINT =
0.0000
I donot understant ehy the energy is so high? this happens with almost all
the crstal structures that i use.
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Received on Fri Nov 25 2011 - 03:30:02 PST
