AMBER: questions about topology file

From: Fabien CAILLIEZ <>
Date: Fri, 1 Jul 2005 17:49:20 +0200 (CEST)

Dear all,

I have few questions about AMBER topology files.

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 ?

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.

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.

Thamk you in advance for your answers,
The AMBER Mail Reflector
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Received on Fri Jul 01 2005 - 17:53:01 PDT
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