AMBER Archive (2008)

Subject: Re: AMBER: amber :antechamber problem

From: Wei Chen (
Date: Mon Jan 07 2008 - 10:14:53 CST


Probably you didn't add all hydrogen atoms on heavy atoms to avoid nonpaired
electrons. Or you can use -j 5.

Wei Chen

On Jan 4, 2008 10:51 PM, jani sahil <> wrote:

> 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,

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