Antechamber was designed to generate parameters for small molecules or
fragments, definitely *not* the kind of molecule you are using. Can't
you just use GAFF parameters for it?
Gustavo.
On Thursday, October 14, 2010, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
> Hello,
>
> I built a single layer of graphite according to the crystal operation.
> And I tried to generate the parameter file for it with antechamber.
> When I run antechamber as following, I got this error.
>
> antechamber -fi pdb -fo mol2 -i grap2.pdb -o grap2.mol2
> -------------------------------------------------------------------
> The atom number exceeds the MAXATOM, reallocate memory
> Info: the bond number exceeds MAXBOND, reallocate memory automatically
>
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> Info: the actual number of rings (72588) 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
>
> Error: cannot run "/home/bkim/packages/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit
> ------------------------------------------------------------
>
> I attached the input pdb file of graphite.
> If you have any idea to avoid this error, please let me know.
> Thank you.
> Bongkeun Kim
>
>
--
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 14 2010 - 14:30:02 PDT
