Hi,
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"
The problem is that I obtain the follow message:
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
---------------------------------------------------
* NB pairs 1726 52366155 exceeds capacity ( 52366666)
SIZE OF NONBOND LIST = 52366666
SANDER BOMB in subroutine nonbond_list
Non bond list overflow!
check MAXPR in locmem.f
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
and still not working.
May I use the pmemd.mpi ? or what I have to check to solve the error?
Thank you
Anna
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 25 2016 - 02:30:03 PST
