Tutorial-l Mailing List

From: Timothy Isgro (timisgro_at_ks.uiuc.edu)
Date: Mon Jul 17 2006 - 11:19:02 CDT

Hi Rita,

> Dear Sirs,
>
> I've started working with NAMD and VMD programs for almost 3 months
> and
> i've almost finished the tutorials of both programs. I have two
> questions:
> 1) Is there any kind of tutorial or example of simulation with NAMD/
> VMD of
> non organic molecules, specially using AMBER force field instead of
> CHARMM?

We do not currently have a tutorial or example of a simulation of a
non organic with the AMBER forcefield, but such a simulation is
possible. NAMD has the ability to use the AMBER forcefield:
http://www.ks.uiuc.edu/Research/namd/2.6b1/ug/node15.html
You would need to supply an AMBER parameter file for NAMD to use,
which means you will have to construct your own parameters if they
are not available for your molecule. We have some tutorials on
developing parameter and topology information available at the
following page under Science topics:
http://www.ks.uiuc.edu/Training/Tutorials/

> 2) I would like also to know if it's possible to solvate a non organic
> molecules (Pheophorbide) in a solvate different from water? Does NAMD
> offer different kinds of "solvate" or the one who works with the
> program
> has to develop one?

Solvating a molecule for any solvent is automated in the same way
that solvating in water is. However, again this should be possible
to do as long as you have parameters for the solvent. If would just
take some work developing a script which would place the solvent
around your molecule. I think you should forward your email to the
NAMD mailing list (specifically question 2), since there someone
might be able to provide more experience on solvating a molecule with
something other than water.
http://www.ks.uiuc.edu/Research/namd/mailing_list/

> I would be very glad if I can get an answer.
>
> Sincerely yours,
>
> Rita Leite
> (Depart. Photobiophysik HU-BERLIN)

Hopefully, this points you in the right direction.

Regards,
Tim Isgro
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