On Thu, Sep 07, 2023, KAJAL ABROL via AMBER wrote:
>Relaxation of the explicit water system, and my protein showed some of the
>energies with ************* in the minimization output file.
>
>
>I used this minimization script:
>
>minimization of solvent
> &cntrl
> imin = 1, maxcyc = 1000,
> ncyc = 1000, ntx = 1,
> ntwe = 0, ntwr = 500, ntpr = 50,
> ntc = 1, ntf = 1, ntb = 1, ntp = 0,
> cut = 10.0,
> ntr=1, restraintmask = ':1-173',
> restraint_wt = 100.,
> ioutfm=1, ntxo=2,
> /
>
You need to turn on SHAKE (set ntc=ntf=2) in order to run explicit solvent
simulations.
There may be other problems (you initial structure has some really bad
contacts), but turning on SHAKE is the first thing to try.
....dac
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Received on Sat Sep 09 2023 - 12:30:02 PDT
