Dear David,
Thanks for your suggestion and I'm sorry for late reply. It seems
`ntc=2` fix the problem.
But I'm wondering why only TIP4P-D requires this parameter while the
Amber 14 manual said
> Since SHAKE is an algorithm based on dynamics, the minimizer is not
aware of what SHAKE is doing; for this
> reason, minimizations generally should be carried out without SHAKE.
One exception is short minimizations
> showse purpose is to remove bad contact before dynamics can begin.
Because of this, following my minimization steps were performed with
default `ntc=1`:
1. Minimizeation of H atoms on the protein and solvent molecules (ntr=1,
restraintmask='.N=,C=,O=,S=,Na=,Cl=')
2. Minimization of Na+, Cl- and solvent molecules (ntr=1,
restraintmask=:<PROTEIN>)
3. Minimization of the system (ntr=0)
And applying `ntc=2` at the initial step solve the problem.
So is my case an exception or `ntc=2` should be performed for the
initial minimization step generally?
Thanks for taking time.
Asai
On 07/29/2016 07:46 AM, David A Case wrote:
> On Thu, Jul 28, 2016, Suguru ASAI wrote:
>> EEL value in mdout become ******* in minimization and a program failed.
>> I would like to solve this problem but don't know where to check or how
>> to fix.
> Something bad is happening around atoms 560 and 570. Have you set ntc=2
> in your input file? This is required for rigid water models. Otherwise
> you can get hydrogens arbitrarily close to oxygens on neighboring molecules.
>
> ....dac
>
>
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Received on Sun Jul 31 2016 - 21:30:02 PDT
