AMBER Archive (2008)

Subject: Fwd: Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files

From: FyD (
Date: Thu Oct 09 2008 - 11:57:07 CDT

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     Date: Thu, 09 Oct 2008 18:56:25 +0200
     From: FyD <>
Reply-To: FyD <>
  Subject: Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER
trajectory/coordinate files
       To: Robert Hanson <>

Quoting Robert Hanson <>:

> I see. Basically an atom would have a name and an "alternative" name. That
> would be easy enough to implement. Charges are already displayable in this
> way within Jmol -- and can be the basis for coloring atoms or isosurfaces
> (molecular surfaces, solvent-accessible surfaces, etc.). In the Jmol
> documentation, search for "charge".

ok, we will update our Jmol version.

> You mean just read the FLAG AMBER_ATOM_TYPE field? That's easy enough. I
> could do that very quickly.

This is indeed what you need for the topology file format (prmtop).

However, this will be obviously different for the "Tripos mol2", the
XLEaP "OFF" and the "prep" file formats...

> We could certainly make that field selectable as well. For example,
> select carbon and not atomType=C3

This is indeed quite simple for the CT atom type but more complex for
other atom types.

> Sounds like I need to get that list of AMBER atom types. Does that list
> allow clear differentiation between CA (alpha carbon) and CA (calcium), for
> example? HE (hydrogen) and HE (helium)? etc.?

See Cornell et al. J.Am.Chem.Soc. 1995, 117, 5179-5197.
See table 1: page 5182

> I have a general question about these files:
> Is a reader of a topology file supposed to totally ignore the %FLAG lines
> and just know that certain fields are in certain places in a certain order?
> That is, are these just comments for the occasional human reader of the
> file, or are they directives that are part of the file specification? (Can I
> depend upon them being there? Can I depend upon their formats being the
> same?)


If you do a google search using FLAG AMBER_ATOM_TYPE from, you will get a lot information...

regards, Francois

----- End forwarded message -----

           F.-Y. Dupradeau

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