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

From: Robert Hanson <>
Date: Thu, 9 Oct 2008 08:59:20 -0500

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".

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

We could certainly make that field selectable as well. For example,

  select carbon and not atomType=C3

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.?

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


On Thu, Oct 9, 2008 at 2:26 AM, FyD <> wrote:

> Dear Bob,
> Q: Tell me more about what "display force field atom types" means. There
>> is
>> an algorithm in Jmol that attempts to match an atom type specified in
>> terms
>> of a PDB atom name to an element. It's used in both its mol2 reader and in
>> the AMBER topology file reader. So if it works in one (or doesn't!) then
>> it
>> should (or won't!) in the other. I notice that even VMD makes mistakes
>> there,
> I do not think VMD can display force field (FF) atom types, i.e. the atom
> types specific to a particular FF !
> so I have to think not specifying the element is a flaw in the
>> topology file spec. Or am I missing something?
> You could adopt 2 different strategies for the selection of the FF atom
> types in a file format:
> 1) Decide to not read the FF atom types (_if_ available in the considered
> file format), but predict them based on some "chemical group/motif
> recognition". This is a lot of work, but this is very inportant for force
> field developers as in the AMBER mailing list... If you wish to do that for
> the AMBER FF (for CHARMM FF, the rules would be different). I can help you
> as I know by heart the AMBER FF atom types ;-)
> 2) Decide to 'simply' read the part of the file where the FF atom types are
> stored.
> Q: Define "display." Do you mean "label by"? "select by"? "color by"?
> By display, I thought "yes" a label... To be able to display "FF atom
> types" or even "atomic charges" as we display "atom names".
> Let's take an example: We use Jmol 10.2.0 .
> You click right & you pick up "Labels/With Atom Names"
> We would do the same for "FF atom types" & "atomic charges"
> Labels/Atom Names
> but also
> Labels/Atomic charges
> Labels/Force field atom types
> Q: Jmol certainly reads mol2 files, and if those mol2 files have PDB
>> residue
>> specifications, then it reads those. Is that what you mean?
> Please see below.
> Q: Jmol also reads cml files. But there is quite a bit of variation in
>> that
>> standard. So I would have to look at the specific files you have in mind
>> to
>> answer you. Can you send me (off-list) a few sample files?
> Let's take an example for th Tripos mol2 file format:
> 1 C1 1.352237 -0.856933 0.225852 C 1 DMSO -0.2897
> (1) (2) (3)
> (1) atom names
> (2) FF atom types - in this case this is only the chemical symbol but this
> is the FF atom type column, do not worry ;-)
> (3) atomic charges
> best regards, Francois
> F.-Y. Dupradeau
> ---

Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Received on Sun Oct 12 2008 - 05:09:36 PDT
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