Hi list.
At the end, I did not manage minimize the problematic waters so I simply
removed them.
Best.
Petro.
On Thu, Jan 9, 2020 at 10:54 AM Petro <subscribe.khoroshyy.net> wrote:
> Hi List.
> After adding water by addtobox to a pDB and ruining minimization I still
> have some overlapping water hydrogen. For now I came up with a crude
> solution and remove these 2-4 waters. But is there any way I can force
> minimization to solve it?
> here is my minimization parameters :
> """
> simple generalized Born minimization script
> &cntrl
> imin=1, ! initiate minimization
> ntb=1, ! use NVT ensemble
> maxcyc=100000,
> ncyc = 3000, !was 1000
> ntpr =10,
> cut=12.0, ! cutoff 12 Ang
> ntr=1, ! weak positional restrains
> iwrap=1
> /
> Keep protein fixed with weak restraints
> 10.0
> RES 1 {0}
> END
> END
>
> The output of minimization repeatedly tells
> .... RESTARTED DUE TO LINMIN FAILURE ..
>
> Thank you.
> Petro
>
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Received on Tue Feb 04 2020 - 05:00:02 PST
