AMBER Archive (2009)

Subject: Re: [AMBER] specification of antechamber AC file format?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Mar 04 2009 - 16:39:44 CST

On Tue, Mar 03, 2009, Nicholas Musolino wrote:
>
> As a matter of fact, I have MOL2 files with SYBYL atom names and
> complete bond information, which I generate in an automated way. But no
> matter what I try, I can't seem to do a straight conversion of this
> information to .AC format through antechamber. (I also want to add
> partial charges, but that's not a huge problem.)

Can you provide an example that fails?

>
> Right now I am looking to bypass antechamber and write my own .AC files
> for use with parmchk.

It's not clear why you need to write .ac files, which are not really
intended as a general file format (and it would be good to get rid of
them). The parmchk program can use mol2 files as input, and you seem to
already have them. Of course, parmchk doesn't know about the sybyl
force field, so you do need to use antechamber to convert the atom
types.

Which returns us to the original question -- what is going wrong with
Antechamber itself?

...dac

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