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 Thu Jan 09 2020 - 02:00:01 PST
