[MMTK] Two proteins in a universe

vanitha@cs.wisc.edu vanitha at cs.wisc.edu
Thu Feb 23 19:33:56 CET 2006


Thanks. If Protein 1 has N atoms, and Protein 2 has M atoms, the
configuration vector will then be a 3(N+M) X 1 vector. Can I safely assume
that the first 3N X 1 entries will correspond to Protein 1 and the last 3M
X 1 entries will correspond to Protein 2 provided Protein 1 was added to
the universe before Protein 2.
I need update the configuration vector for Protein 1 differently from that
of Protein 2 and it will help to know this!

Thanks,

- Vanitha

> On Feb 23, 2006, at 16:58, vanitha at cs.wisc.edu wrote:
>
>> If I add two proteins to a universe, can I get the configurations
>> and the
>> gradients of the two separately and update them separately if
>> required? My
>> goal is to miminize the energy of the complex in a space other than
>> the
>> cartesian co-ordinates. Can I eventually write the complex out to a
>> single
>> PDB file?
>
> A configuration object is always for a whole universe. However, you
> can access and modify the configuration atom by atom if you want, so
> nothing stops you from handling the two proteins in the universe
> separately. And if you write the whole universe to a PDB file, you
> will obviously get both proteins in it.
>
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire Léon Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: konrad.hinsen at cea.fr
> ---------------------------------------------------------------------
>
>
>
>





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