Hello Jesmita,
It appears that your molecule is very very big. Try using a smaller
analogue of your larger graphene oxide sheet - one that captures the unique
chemical functionalities (e.g. bonds, angle and torsions). Run this smaller
analogue into antechamber to get some suggestions for parameters. If you
have correctly accounted for all of the unique internal coordinates in your
analogue, then the resulting parameters "should" be transferable to the
larger sheet. The one thing that might need some additional consideration
is the partial atomic charges, and if your analogue captures the
delocalization that is present in the larger sheet.
Bests,
Karl
On Thu, Feb 25, 2016 at 10:36 AM, Jesmita Dhar <dhar.beauty.gmail.com>
wrote:
> Hello,
> We are getting the following error while we have run antechamber to
> generate the parameter file for graphene oxide.Pls help me
> Info: the bond number exceeds MAXBOND, reallocate memory automatically
>
> Info: the bond number exceeds the MAXBOND, reallocate memory, automatically
> Info: the actual number of rings (7134) exceeds the defaut ring size
> (500), reallocate memory automatically
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase PSCUTOFF in define.h and recompile bondtype.c
> Be cautious, use a large value of PSCUTOFF (>100) will
> significantly increase the computation time
>
> Info: the bond number exceeds the MAXBOND, reallocate memory, automatically
> Info: the actual number of rings (7134) exceeds the defaut ring size
> (500), reallocate memory automaticallyTotal number of electrons: 3931;
> net charge: 1
> INFO: Number of electrons is odd: 3931
> Please check the total charge (-nc flag) and spin multiplicity (-m
> flag)
>
> Running: /home/pinak/amber14/bin/sqm -O -i sqm.in -o sqm.out
> Error: cannot run "/home/pinak/amber14/bin/sqm -O -i sqm.in -o
> sqm.out" of bcc() in charge.c properly, exit
>
> On Tue, Feb 23, 2016 at 5:04 PM, Jesmita Dhar <dhar.beauty.gmail.com>
> wrote:
> > Dear sir/madam,
> > I have docked graphene oxide to human
> > lysozyme protein. I want to run md simulation, but can not able
> > generate the parameter file using antechamber as its very large
> > sturcture.
>
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--
Karl. N. Kirschner, Ph.D.
Research Associate
Bonn-Rhein-Sieg University of Applied Sciences
Grantham-Allee 20, 54757 Sankt Augustin, Germany
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Received on Thu Feb 25 2016 - 02:00:04 PST
