Re: [AMBER] antechamber is failing for a molecule

From: case <>
Date: Thu, 20 Jan 2011 11:59:52 -0500

On Wed, Jan 19, 2011, Alan Wilter Sousa da Silva wrote:

> I am trying to run antechamber for an specific mol and I am getting this
> error:
> antechamber -i TB11_noprot.pdb -fi pdb -o TB11_noprot_bcc_gaff.mol2 -fo mol2
> -c bcc -nc -2 -m 1 -s 2 -df 0 -at gaff -pf n

You molecule is rather odd, and it is not too surprising that antechamber has
problems with it. I'm guessing that it is interpreting C9-O1 as a carbonyl,
and thinking that C8 has only three single bonds attached to it.

[I guess you want the O1 atom to be a deprotonted alcohol, and C9-C8 to be a
double bond, but antechamber won't recognize this, and doesn't have parameters
built in for such a system. Can O1 really be deprotonated, especially in the
gas phase??]

> If running the protonated version of the mol with -nc -1 all goes fine.

The protonated version is a much more standard sort of closed-shell organic
molecule. If you need parameters for the deprotonated form, you will probably
have to derive them by hand, since this appears to be outside of antechamber's
range of applicability.

Having said that, you could try playing with the "-j" option, but be sure to
examine any results critically.


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Received on Thu Jan 20 2011 - 09:30:04 PST
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