From: M. L. Dodson <>
Date: Sun, 01 Jul 2007 10:57:05 -0500

Francesco Pietra wrote:
> I came back to this message, now that I have carried out the tutorial sustiva
> with antechamber in amber9.
> I started by investigating which atom is which in the file sustiva.pdb. In my
> work - including when making use of MD - the stereochemistry is at the
> forefront, so that I took sustiva.pdb as a stereochemical exercise, even where
> it is irrelevant. I first changed to the opposite enantiomer, to have that
> displayed at the top of the html on line, then clarified everything. I did
> that with my MM package, after that I was unable to display "atom serial
> numbers" graphically with VMD (it was my first approach to VMD, otherwise that
> should be a standard task for this package).

I guess I don't really understand what you did. I may be entirely off
base, but this seems to not be a very productive exercise. I don't know
what html you are talking about, for example.

> Later on during the tutorial, xleap was a pleasant surprise, as it allows
> detecting which atom is which.

If by that you mean you can click on an atom and get an identification
that maps back to the structure file, every molecular graphics program I
know about allows that.

> To conclude, the mere possibility of identifying rapidly the atoms in the space
> - during the work with amber9, when it would be difficult with the MM package -
> opens to my studies an easier way. On the other hand, I was always the opinion
> that becoming GUI-addict detracts from the wide possibilities that a console
> offers.

Well, as I have opined here, GUI interfaces have their places, but are
most useful only in an appropriate domain of application. I personally
don't make much use of them in the way you describe. If I understand
what you are saying (which I may not).

> Three simple questions arising from the antechamber/sustiva tutorial:
> 1) Why the atom symbol Cl is not left justified at column 13?

Look at the descriptions of the various "interpretations" of the pdb
format in the amber documentation. E.g., in the documentation for
ambpdb or ptraj.

> 2) Why water as solvent for a molecule like sustiva, which looks like to be
> sparingly soluble, if at all, in this solvent? Sometimes water is not the most
> appropriate medium even in the perspective of proteins.

Well, organisms are mostly water, and sustiva is a bioactive compound.
Whether water is the most appropriate solvent is definitely important,
but you always have to start somewhere. I would submit water is a good
starting place, nothing more. The most relevant solvent depends on the
scientific question being posed.

> 3) Where the best and most recent instructions to parameterize what is unknown
> to GAFF? I'll surely have to spend most of my MD-time there. With the aid of
> NWChem, and my experience with, I should be prepared to the task.

I'm not expert in GAFF (please help us out here, folks), but I was under
the impression that, if an organic molecule is not handled by GAFF, that
was to be considered a bug in GAFF. I suggest you ask the developers of
that force field directly. And read their papers.

> Thanks
> francesco pietra

Bud Dodson
M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-five_63-386_one
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jul 04 2007 - 06:07:06 PDT
Custom Search