Try using pmemd instead of sander. Or run sander in serial.
HTH,
Jason
> On Mar 8, 2016, at 5:36 AM, Anna Cebrian Prats <Anna.Cebrian.uab.cat> wrote:
>
> 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 - 05:30:04 PST
