AMBER Archive (2005)

Subject: Re: AMBER: questions about topology file

From: David A. Case (case_at_scripps.edu)
Date: Fri Jul 01 2005 - 15:24:02 CDT

On Fri, Jul 01, 2005, Fabien CAILLIEZ wrote:
>
> The first concerns atom types. In topology file, atom types are defined in
> two places after the flag ATOM_TYPE_INDEX and the flag AMBER_ATOM_TYPE. It
> appears that both are differents. I understand that the first only
> concerns non-bonded interactions and so two atom with a different
> AMBER_ATOM_TYPE can have the same ATOM_TYPE_INDEX (for example HO and HW).
> Am I correct ?

yes.

>
> The second question also deals with AMBER_ATOM_TYPE. What is the use of
> this flag in AMBER ? Because it seems to me that all the parameters for
> the interactions to be calculated are given in the topology file
> independantly of this type.

The TYPE flag is not used inside Sander (I believe), but might potentially be
used by other programs that read prmtop files.

>
> Finally, I wonder if there is any order in the BONDS_WITHOUT_HYDROGEN
> section. For example, can I just add one term at the end of this section
> (and changing of course numbnd value) just by adding the two index for my
> atoms and the type of bond parameters that I want to use.

You should be able to do this.

...dac
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