Thank you! I will have a try.
________________________________________
From: David A Case <case.biomaps.rutgers.edu>
Sent: Saturday, March 8, 2014 1:00 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Antechamber add new parameter
On Sat, Mar 08, 2014, Mengyuan Zhu wrote:
>
> I added more information to gaff.dat file as I thought antechamber would
> recognize my atom boron in my molecule. However, antechamber still has
> error “For atom[104]:B1, the best APS is not zero, bonds involved by
> this atom are frozen”. What shall I do next?
You are not easily going to be able teach antechamber to understand molecules
containing boron. You would have to update the files in
$AMBERHOME/dat/antechamber in appropriate ways. This, in turn, would require
a deep understanding of the way the code works. It's not impossible, but it
would be a major effort.
If you just have one or a few molecules that contain boron, I'd recommend
doing them by hand, or using programs like wolf2pack or R.E.D. to assist you.
See the pointers to these program on the Amber web site.
...dac
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Received on Sat Mar 08 2014 - 10:30:04 PST
