On Thu, Feb 25, 2016, Anna Cebrian Prats wrote:
>
> I am trying to run the minimization with sander
> using a .top file and the inpcrd file as a result of
> using the chamber (executable that convert charmm files to amber files)
> of amber14. The system constitute a large protein with a Fe+2 coordinated with
> 5 residues and a "-OH"
>
> * NB pairs 1726 52366155 exceeds capacity ( 52366666)
How many atoms are in your system. What value of cut did you give in the
input file? (Try the default value if you are using a bigger value now.)
You can certainly try pmemd. Don't do anything in parallel until you can get
the system working correctly in serial mode.
> I already check MAXPR of the locmen.f and try to modify the assignment
> to maxpr_float two the lines below:
>
> >> maxpr_float = natom * (cutoffnb + skinnb)**3 / 2.5d0
> >> to
> >> maxpr_float = natom * (cutoffnb + skinnb)**3 / 1.5d0
Just to be sure: did you re-compile after making this change?
...dac
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Received on Thu Feb 25 2016 - 05:30:05 PST
