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
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Received on Wed Jul 04 2007 - 06:07:06 PDT
