RE: AMBER: antechamber problems

From: Junmei Wang <>
Date: Mon, 20 Jun 2005 11:35:12 -0500

We used different algorithms to assign bond types in amber7 and amber8. Please use option "-j 5" for your molecule to generate the prepi file. We are doing some revision to make the programs work better for molecules that have many possible valence states (according to our definition)

All the best


Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649

-----Original Message-----
From: [] On Behalf Of hj zou
Sent: Friday, June 17, 2005 8:32 AM
Subject: AMBER: antechamber problems

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,
The AMBER Mail Reflector
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Received on Mon Jun 20 2005 - 17:53:08 PDT
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