AMBER Archive (2008)

Subject: Re: AMBER: antechamber problems

From: Junmei Wang (junmwang_at_gmail.com)
Date: Sat Jan 05 2008 - 23:35:04 CST

Your molecule has open valence, please fill in the open valence with
hydrogen atoms first. Antechamber can only handle molecules without open
valence.

Junmei

On Jan 4, 2008 9:49 PM, jani sahil <genomejani_at_gmail.com> wrote:

>
>
> Hello
> 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
>
>
>
>

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