Dear Amber users,
I am using the antechamber tool. But when typing the command
$AMBERHOME/exe/antechamber -i filename.pdb -fi pdb -o prepin -fo prepi
-c bcc -s 2, it is showing the message:
The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically
Running: /usr/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0
-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 (3880) 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 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 "/usr/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
and the program stops here. I am attaching my pdb file and the files generated.
can you please tell me how to get rid of the problem?
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Received on Tue Jun 26 2012 - 01:00:03 PDT
