----- Forwarded message from fyd.q4md-forcefieldtools.org -----
Date: Thu, 09 Oct 2008 18:56:25 +0200
From: FyD <fyd.q4md-forcefieldtools.org>
Reply-To: FyD <fyd.q4md-forcefieldtools.org>
Subject: Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER
trajectory/coordinate files
To: Robert Hanson <hansonr.stolaf.edu>
Quoting Robert Hanson <hansonr.stolaf.edu>:
> 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).
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
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?)
See: http://ambermd.org/formats.html
If you do a google search using FLAG AMBER_ATOM_TYPE from
http://archive.ambermd.org/, you will get a lot information...
regards, Francois
----- End forwarded message -----
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Oct 12 2008 - 05:10:05 PDT
