AMBER Archive (2007)

Subject: AMBER: Problem generating .prepin file in Antechamber

From: Lili Peng (lilipeng_at_gmail.com)
Date: Thu Aug 02 2007 - 14:07:11 CDT

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.cproperly, 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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