I have also included the pdb file, should it be useful.
On 8/2/07, Lili Peng <lilipeng.gmail.com> wrote:
>
> Dear all,
>
> I am having problems generating a prepin file in antechamber. I created a
> structure in Chemdraw, saved it in PDB format, but when I try running
> antechamber, I get the following error message:
>
> "The atom number exceeds the MAXATOM, reallocate memory
> Info: the bond number exceeds MAXBOND, reallocate memory automatically
>
> running: /usr/local/apps/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.ACO
> -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
> Info: The atom number exceeds the MAXATOM, reallocate memory automatically
>
> Info: The actual number of rings (1022) exceeds the defaut ring size
> (500), reallocate memory automatically
>
> For atom[1096]:0, the best APS is not zero, exit
> For atom[1096]:0, the best APS is not zero, exit
> For atom[1096]:0, the best APS is not zero, exit
> For atom[1096]:0, the best APS is not zero, exit
> For atom[1096]:0, the best APS is not zero, exit
> For atom[1096]:0, the best APS is not zero, exit
> For atom[1096]:0, the best APS is not zero, exit
>
> 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 MAXVASTATE in define.h and recompile bondtype.C
> (4) increase PSCUTOFF in define.h and recompile bondtype.C
> Be cautious, use a large value of PSCUTOFF (>10) will significantly
> increase the computer time Error: cannot run
> "/home/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
> ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of
> antechamber.c properly, exit
> "
>
> Does anyone have any ideas what may be the underlying problem? My
> intuition is telling me that it's something to do with the way I drew the
> structure in Chemdraw, but I don't know where to begin . Any comments or
> guidance would be greatly appreciated.
>
> Thanks,
> Lili
>
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Received on Sun Aug 05 2007 - 06:07:38 PDT
