Re: CG Name Prefix Problem

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Fri Oct 24 2008 - 10:30:05 CDT

Hi Anirban,

Usually, viruses consist of many copies of one or a few identical
proteins. What you need to do is to coarse-grain each of these unique
proteins, and then map the coarse-grained model onto other copies of
the same protein.

There is an SBCG mapping tool in VMD, together with other coarse-
graining tools in the CG Builder. If you cannot find it in your
version of VMD, download the latest VMD test version here:

http://www.ks.uiuc.edu/Research/vmd/alpha/

Please see also the description of VMD CG tools here:
http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/

To make things clearer, here is an example. Let's say you need to work
with a virus that consists of 60 copies of protein 1, 60 copies of
protein 2, and 60 copies of protein 3. Then, use SBCG Builder to
create a CG model of one copy of protein 1, using the CG name prefix
"A"; do the same for protein 2, using the CG name prefix "B"; and the
same for protein 3, with the name prefix "C". Then use the SBCG
mapping tool on the CG model with names "A", to obtain PDBs of the
rest 59 copies of protein 1. Do the same for the remaining 59 copies
of protein 2 (using the CG model with names "B"), and for the
remaining 59 copies of protein 3 (using the CG model with names "C").

As a result, you will have 60 copies of the CG protein with names "A",
the same for "B", and same for "C". The copies will have different
segnames after you assemble the structure together using psfgen.

This is essentially the same as in the case of an all-atom structure.
If you think about the same example with proteins 1, 2, and 3, the all-
atom structure of the virus contains, e.g., 60 copies of protein 1,
the copies differing from each other only by the coordinates of their
atoms and by their segnames.

Best,

Anton.

On 24 Oct 2008, at 00:24, Anirban Ghosh wrote:

>
> Hi ALL,
>
> I want to build a CG model for a virus particle consisting of 70
> chains.
> The VMD CGTools plugin is unable to generate a Shape Based CG model
> if I
> upload the entire PDB file at once. So I divided the file into 70
> parts
> according to the chains. Now when I need to specify a "CG Prefix Name"
> which should be a single character one in the CGTools plugin. I cannot
> give numerals as they will become 2 characters after 9 and also
> there are
> only 26 alphabets! So how should I differentiate between the chains
> and
> what should I give in the CG Prefix Name for the individual chains?
> Please
> suggest.
>
> Regards,
>
> --
> Anirban Ghosh
> Grade Based Engineer
> Bioinformatics Team
> Scientific & Engineering Computing Group
> Centre for Development of Advanced Computing
> Pune, India
>

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