Dear Amber Users,
I am using Amber 9.0 version. My system contains molecule having
benzene ring as a part of it.My leap went through with some unusual warnings
like '*1-4: angle 12388 12392 duplicates bond ('triangular' bond) or angle
('square' bond)' *and leap generated pdb looks fine ( generated using
'savepdb' command in leap). But during the very first minimization itself
some bonds in the benzene ring seen to be broken and energy bounds up with
very high positive values ( part of the output file and input is given
below). What could be the reason for the breaking of bonds in benzene
ring?. Is there any problem leap?. why the system have high positive
energy?. Can anyone help me in figure out these problems. Waiting for your
valuable reply.
*************************************************************
*Input file*
&cntrl
imin = 1, maxcyc = 2000, ncyc = 1000, ntr = 1, ntb =1,cut = 12.0
&end
************************************************************************
*output*
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 4.3335E+04 3.2420E-01 9.9189E+00 C1 6289
BOND = 325.9711 ANGLE = 9200.0268 DIHED =
10662.7695
VDWAALS = -656.7634 EEL = -27379.6446 HBOND =
0.0000
1-4 VDW = 988.0315 1-4 EEL = 50194.7959 RESTRAINT =
0.0000
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 4.3335E+04 3.2420E-01 9.9189E+00 C1 6289
BOND = 325.9711 ANGLE = 9200.0268 DIHED =
10662.7695
VDWAALS = -656.7634 EEL = -27379.6446 HBOND =
0.0000
1-4 VDW = 988.0315 1-4 EEL = 50194.7959 RESTRAINT =
0.0000
***********************************************************************************************************
Thanks in advance
Aneesh
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Received on Wed May 20 2009 - 14:15:45 PDT
