AMBER Archive (2005)

Subject: AMBER: antechamber problems

From: hj zou (hjzou_at_iris3.simm.ac.cn)
Date: Sun Jun 19 2005 - 08:50:08 CDT

Dear amber users£¬

        I run into a problem when I try to produce ligand prep file from gaussian output file by using antechamber in AMBER8.0
    The following is what I did:
    
antechamber -i test.log -fi gout -o test.prep -fo prepi -c resp -nc -1

Cannot successfully assign bond type for this molecule, 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

    Most of atom types in the output file test.prep are wrong. I have checked the structure of the ligand. It is OK. Moreover, the antechamber in AMBER7.0 works fine for this ligand. What's wrong?
    The ligand is NAD+, which I have enclosed as attachment.
    Can anyone tell me how to deal with it? Thank you in advance.
   Best regard,


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