VMD-L Mailing List

From: Boris Steipe (boris.steipe_at_utoronto.ca)
Date: Wed Oct 01 2008 - 11:37:48 CDT

Your atoms are labelled with three character so that every one has a
unique label in the molecule.

The first character is the element code. You have carbons, nitrogens
and hydrogens.

The second character characterizes the topology of the atom. A
typical sequence counting outward, or around the ring might follow
roman character for the greek alphabet: A B G D E Z H ... (this looks
like the PDB convention for amino acids), some of your atoms seem to
be counting 1 2 3 4 5 ... (this looks like the PDB convention for
nucleotides, or some hetero-groups) In PDB files, H-atoms are often
labeled according to the carbon they are bound to. Your hydrogens do
not follow that convention.

The third character is an index, in case more than one atom is bound
to a single other, as in HA1, HA2 ...

If this is not the information you were asking about, please explain
what exactly you mean by "type of atom".

B.

On 1-Oct-08, at 12:28 AM, Rudra Banerjee wrote:

> dear friends,
> this might be an idiotitic question but i have tried a lot and
> failed to get a result (so please dnt scold on me). Below is the
> representation of the molecule i am working on.
> HE1 H1 H4
> | | |
> HA2 HD1 CE1 C1 C4 H5 H83
> | | // \ / \\/ \\/ |
> HA1-C10 CD1 CZ C2 C5 C8-H82
> / \ | || | | | \
> HA3 N2-CG CE2 C3 C6----N1 H81
> / \\ / \ //\ // \
> HB1-C11 CD2 N C7 C9-H93
> / \ | | / \
> HB2 HB3 HD2 H7 H91 H92
>
> Having very little knowledge on organic chemistry, I am not getting
> what type of atom is the N2,C10,C11 AND CG (and similarly
> C6,N1,C8,C9).
> Is there anyone who could help me?
>
>
>
> --
> Rudra
> JRF; SNBNCBS
> http://www.bose.res.in/~rudra
>
> A bus station is where a bus stops. A train station is where a train
> stops. On my desk I have a work station.
>
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> Why?See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
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