AMBER Archive (2008)

Subject: Re: AMBER: How to confirm atom types of small molecule perceived by antechamber

From: Junmei Wang (junmwang_at_gmail.com)
Date: Mon Jun 23 2008 - 09:57:18 CDT

Hi, Xiaonan,
Antechamber atom types are described in the force field file (gaff.dat).
More details are on the gaff paper (J Comput Chem 25: 1157–1174, 2004). You
may also take a look at the ATOMTYPE_GFF.DEF file in the dat/antechamber
directory for strict definitions.

Best

Junmei

On Mon, Jun 23, 2008 at 3:39 AM, xiaonan zhang <heptoking_at_gmail.com> wrote:

> Dear All
> I'm learning to use antechamber (AMBER 9) to simulate
> protein-inhibitor complex. After reading the tutorial,
> I managed to prepare topology and coordinate files for a complex.
> However, I am still nervous about the validity of the atom types and
> bond order assigned to the inhibitor.
> the prepin file have the atom types for every atom, but unfortunately I
> cannot understand it because there
> are no description about the naming conventions of these atom types in the
> manual.
>
> Can anybody tell me where can I find the definition of these atom
> types?? Or are there any other ways to
> easily identify the bond orders or atom types?
>
>
> Thank you!
>
>
> Xiaonan Zhang
> Shanghai public health clinical center
>
>
>
>
>

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