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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Received on Thu Feb 25 2016 - 02:00:03 PST
