Hi
I am running minimization in two steps,
1-only ligand restrained
2-all atom free
in step 1:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -2.0430E+03 2.8422E+01 4.8010E+02 C10 12
BOND = 355.9089 ANGLE = 631.5501 DIHED =
8.1372
VDWAALS = 589.0436 EEL = -3742.7066 HBOND =
0.0000
1-4 VDW = 4.9766 1-4 EEL = 110.1086 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -4.9406E+03 2.6839E-01 3.5606E+00 C1 2
BOND = 408.4399 ANGLE = 365.8105 DIHED =
12.6880
VDWAALS = 1023.2659 EEL = -7058.3052 HBOND =
0.0000
1-4 VDW = 4.5455 1-4 EEL = 102.4656 RESTRAINT =
200.4677
EAMBER = -5141.0898
and my structure is ok!
I use this input for step 2;
polyA-polyT 10-mer: initial minimization whole system
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 1000,
ntb = 1,
ntr = 0,
cut = 10.0
/
but I have a large EEL ( NSTEP ENERGY RMS GMAX
NAME NUMBER
1000 -1.1481E+08 9.8473E+11 4.0081E+13 Fe1 1
BOND = 640.8838 ANGLE = 111.2013 DIHED =
45.9424
VDWAALS = 1045.9443 EEL = ************* HBOND =
0.0000
1-4 VDW = 4.6864 1-4 EEL = 77.0429 RESTRAINT =
0.0000)
can you help me?
I only have ligand with water!
or when I do the heating step, I have
"vlimit exceeded for step 4516; vmax = 23.5159"
I don't know How solve it! I read
(
http://archive.ambermd.org/201210/0430.html)
but for my case don't have the answer!
thanks a lot
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Received on Sun Feb 07 2016 - 05:00:04 PST
