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 (ntc=ntf=2) in order to carry out explicit solvent
simulations.
There may be other problems, since you starting structure have some very bad
close contacts, but SHAKE is the first thing to try.
....dac
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Received on Sat Sep 09 2023 - 12:30:03 PDT
