[AMBER] Chamber tool, error using the prmtop and inpcrd files

From: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
Date: Tue, 8 Mar 2016 10:36:47 +0000

Hello,


I am working with a big molecule (5-LOX) that has a coordinate sphere with a Fe (III).


I already have the .top, parm., psf and crd files in Charmm22 format. The .top and .parm file where create by using Charmm- Gui.


For that reason, I used the chamber tool as this way;


chamber -cmap -top $PBS_O_WORKDIR/top_lox5.rtf -param \

$PBS_O_WORKDIR/par_lox5.prm -psf $PBS_O_WORKDIR/pdb_lox5_wat.psf \

-crd $PBS_O_WORKDIR/Lox5_wat.pdb -p 3o8y_w.prmtop -inpcrd 3o8y_w.inpcrd \ -box 90.0 95.0 93.0 -vmd -radius_set


And I obtain the added output file


It seems that the prmtop and inpcrd created are correct. Moreover, I visualize the vmd_prmtop that I obtain and the coordinate sphere have the correct interactions.


However, when I plot the minimization using the vmd_prmtop and the inpcrd files, I obtain the following error.


- input file



    Minimization - protein and metal Fe+2
&cntrl
 imin=1, maxcyc=200, ntpr=5,
&end


- Error

--------------------------------------------------------------------------------
   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 416 52366507 exceeds capacity ( 52366666)
     SIZE OF NONBOND LIST = 52366666
 SANDER BOMB in subroutine nonbond_list
 Non bond list overflow!
 check MAXPR in locmem.f


Thank you in advanced for you help


Sincerely,


Anna Cebrián


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 08 2016 - 03:00:03 PST
Custom Search