VMD-L Mailing List

From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Thu Oct 02 2008 - 12:14:25 CDT

no no...you misunderstood my question. I was not seeking help on nomenclature of atom. rather i need to specify the atom type of the said atoms so that there is bond given in parameter file.

  

-- 
Rudra
JRF; SNBNCBS
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----- Original Message ----
From: Boris Steipe <boris.steipe_at_utoronto.ca>
To: Rudra Banerjee <bnrj.rudra_at_yahoo.com>; vmd mailing <vmd-l_at_ks.uiuc.edu>
Sent: Wednesday, 1 October, 2008 10:07:48 PM
Subject: Re: vmd-l: atom type
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.
>
> Please, if possible, don't  send me MS Word or PowerPoint attachments
> Why?See:  http://www.gnu.org/philosophy/no-word-attachments.html
>
>
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