From: Francesco Pietra (
Date: Sun Jul 01 2007 - 02:33:20 CDT

The "small" organic molecule is at the forefront of my problems with MD, and I
need to locate the atoms in space with respect to the "atom serial number" in
pdb files.

I have loaded into VMD 1.8.6 the molecule in attachment (which makes part of
amber tutorials), I have printed the pdb file, noticed that it it is an
abridged form of pdb file and that, even in this restricted form, it digresses
from pdb rules (atom Cl, for chlorine, should be left-justified at column 13).

This is no criticism, it is only to learn how to refine pdb files for my
unpublished organic molecules in view of MD.

As taking into account stereochemistry is a must in my studies, may I ask
advice in locating the atoms in space through VMD 1.8.6? Though it is
irrelevant to the case in attachment, this one will teach me how to deal with
cases where stereochemical assignments are relevant.

I have read about the "atom select" command of VMD. Is that the way? Is any
possibility of graphical output on the VMD screen of the "atom serial number",
or anything that can be related to that? In practice, I want to know which is
which for H3/H4, F1/F2/F3, and so on.

francesco pietra

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