VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jan 16 2008 - 11:02:32 CST

On Jan 16, 2008 4:09 AM, Lucie Huynh <luciehuynh_at_gmail.com> wrote:
> Hi everyone,
>
> I'd like to modify my membrane model by replacing some lipid by a very
> similar molecule.
> Does a "replace" cmd or something like that exist?

well, not in VMD directly, as it assumes that the number and type
of atoms does not change.
however, when using the psfgen plugin, it is possible to delete
atoms and read in new atoms (as additional segments).

> Is it possible to set coordinates to some atoms of a molecule and move the
> entire molecule relatively to the new set of coordinate of these few atoms?

to change coordinates of atoms, one can use selections and set
the coordinates individually.

the problem with all that is, that you have to use tcl scripting and
that there is no pre-existing script to do what you want right away.
if you have a look at the psfgen related tutorials and the solvate
plugins, you should be able to get some ideas on how this could
be done.

good luck,
    axel.
> Thanks a lot in advance for any help,
>
> Lucie
>
>
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.