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
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Received on Tue Mar 08 2016 - 03:00:03 PST
