AMBER Archive (2008)

Subject: AMBER: amber :antechamber problem

From: jani sahil (genomejani_at_gmail.com)
Date: Fri Jan 04 2008 - 21:51:56 CST

Hello amber user
   I got a problem when I try to produce ligand prep file using antechamber
in AMBER8.0
    The following is what I did
antechamber -i inb.pdb -fi pdb -o inb.prepin -fo prepi -c bcc -s 2

the following error I got
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

I am attaching input file.

Can anyone tell me how to deal with it? Thank you in advance.
   Best regard,
 JANI VINOD


  • chemical/x-pdb attachment: inb.pdb
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