On Sun, Feb 07, 2016, Fatemeh Sadat Alavi wrote:
>
> 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?
Hard to be very sure with so little information. You should examine the
structure after 1000 steps, and look for bad contacts, especially at the Fe1
(iron?) atom.
One thing to try: turn on SHAKE (ntc=2). You will need this for dynamics
anyway (all common Amber water models are rigid ones), and it could be that a
hydrogen from some water is getting too close to some other atom. There
could also be some problem with the force field you created for the ligand.
...good luck...dac
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Received on Sun Feb 07 2016 - 05:30:03 PST
