AMBER Archive (2007)

Subject: Re: Fwd: RE: Re: AMBER: on PATH

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sun Jul 01 2007 - 09:38:03 CDT

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_at_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
>

 
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