Thank you to answer.
The system have 10750 atoms including the Fe+2.
The cutoff that I used is the default one, cut=8.0 with igb=0.
Respect to the changes, I recompiled when I made the changes.
But, following jaime 's answer, I already visualize the pdb file with the prmtop obtained using chamber ( that convert the charmm files to the amber files), and the protein don't have connectivity all the atoms appear with any bond connection, so as individual atoms.
Then the problem is with chamber. Then I don't know how to solve it, due to I use the typical usage of the manual amber14.
Anna
________________________________________
De: David A Case <david.case.rutgers.edu>
Enviat el: dijous, 25 de febrer de 2016 14:16
Per a: AMBER Mailing List
Tema: Re: [AMBER] Minimization error using Sander
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 - 06:30:05 PST
