AMBER Archive (2007)

Subject: AMBER: Please check the total charge and your -nc flag

From: snoze pa (snoze.pa_at_gmail.com)
Date: Sun Mar 25 2007 - 22:54:52 CST

Dear Amber Community,

 I am trying to convert a pdb file into mol2 file format using antechamber.
I am using following command
antechamber -i new_POL.pdb -fi pdb -o new_POL.mol2 -fo mol2 -c bcc -nc
NET_CHAEGE -m MULTIPLICITY -j 5 -df 0

but it is not working.. Instead I am getting following error message
Total number of electrons: 255; net charge: 0
Number of electrons is odd: 255
Please check the total charge and your -nc flag
and after this program crashes.

If i will use
antechamber -i new_POL.pdb -fi pdb -o new_POL.mol2 -fo mol2 -c bcc -df 0 &

then error message is different like

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 bondtype etc.

Anyhelp?

thanks in advance

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