From: Francesco Pietra <chiendarret.yahoo.com>
Date: Sun, 1 Jul 2007 13:50:39 -0700 (PDT)

Unfortunately I lost Bud Dodson's kind reply to this message. I do not wish to
make a thread, though I feel compelled to say a couple of words (the last ones
from my side on this matter):

(1) The procedure described below is that of the organic chemist. May be the
organic chemist is out of place in MD, that I can easily concede, if you wish.
However, if you have to deal with molecules embodying a couple of chirality
axes and cycles that flip with them, generating diastereomers from the
conformational motions (and have as major final task to simulate the
solvent-dependent circular dichroic spectrum) you had to share the approach of
the organic chemist.

(2) Atoms of two letters are left justified at column 13 in PDB Format
Description Version 2.2, which is implemented in my MM package (which adopts
the unabridged pdb file type). I simply put a specific question about.

(3)As to the alleged comprehensiveness of GAFF,every organic chemist would
object. Lacking parameterization for, say, carbon carbon triple bond and for
three-membered carbocycles, or having to guess ones as antechamber does in the
tutorial indicated, leaves many thousand of natural products off. A "guess"
can't be equal to parameter determination via QM. Most likely epoxides are also
unknown to gaff, leaving off an equally large number of natural products.
Therefore, I am well prepared to have to have to parameterize for the natural
products that are waiting as pdb files in my machines, and thus my quest for
information. I'll first compare MD outputs with NMR data; if disagreement is
large, I'll first check parameterizations, in particular those guessed, looking
for a better parameterization. This is no criticism to antechamber/gaff,
actually antechamber/gaff, and its integration with the other ff, was great
attraction. Without such kind of tool I could not set up any MD simulation.

Finally, I would say that - in my view - xleap is no GUI in the sense commonly
attributed to GUIs. It starts after a simple "startx" with a minimal window
manager to type a command, and is removed by a simple Ctrl-Alt-Backspace.
Actually, I understand xleap looks as a console that also allows (on request)
to see the molecule or ensemble in 3D. Without such a view, the organic chemist
is largely deprived of his language.

All the best

--- Francesco Pietra <chiendarret.yahoo.com> wrote:

> Date: Sun, 1 Jul 2007 07:38:03 -0700 (PDT)
> From: Francesco Pietra <chiendarret.yahoo.com>
> Subject: Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH
> To: mldodson.houston.rr.com, amber.scripps.edu
> CC: chiendarret.yahoo.com
> 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).
> Later on during the tutorial, xleap was a pleasant surprise, as it allows
> detecting which atom is which.
> 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.
> Three simple questions arising from the antechamber/sustiva tutorial:
> 1) Why the atom symbol Cl is not left justified at column 13?
> 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.
> 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.
> Thanks
> francesco pietra
> --- "M. L. Dodson" <mldodson.houston.rr.com> wrote:
> > You almost never NEED to use xleap. There are only a few things that
> > you can do with xleap that you cannot do with tleap, the "terminal
> > interface" counterpart to xleap. xleap is required primarily for the
> > use of the "edit" and related commands when generating and modifying
> > structures. To prepare input files for the amber simulation programs,
> > you only need tleap. Setting solvent boxes for simulations is NOT a
> > problem for amber, just use tleap. Then you can look at the final
> > product in the molecular graphics program of choice, e.g., vmd.
> >
> > I'll pass along what I have told students learning this program package:
> > put everything possible in shell scripts (which use antechamber, tleap,
> > etc). The scripts (plus the log files) exactly document everything you
> > did and make it easy to reproduce the sequence of steps the next time
> > you need to do something similar. You can even maintain them with a
> > revision control system.
> >
> > Bud Dodson
> >
> > --
> > M. L. Dodson
> > Email: mldodson-at-houston-dot-rr-dot-com
> > Phone: eight_three_two-five_63-386_one
> >
> Don't get soaked. Take a quick peak at the forecast
> with the Yahoo! Search weather shortcut.
> http://tools.search.yahoo.com/shortcuts/#loc_weather

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Received on Wed Jul 04 2007 - 06:07:08 PDT
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