[gmx-users] Re: Question about Gromacs

[Anton Feenstra]

Rahul Banerjee wrote:

> Dear Sir,
>         I am working on protein ligand interaction. I
> am using Gromacs for simulations. I have 2 questions: 
> 1) I have a ligand bound to a receptor. I need to
> check the conformational rigidity of this bound ligand
> by varying only two torsions and calculate the
> resulting energy landscape (Energy vs.torsions). Does
> Gromacs allow me to do this?

If you have some program to produce the rotated conformations
(e.g. in some rasmol versions you can do that manually) you
can use position restraints in gromacs to hold the molecule in
that conformation, or you generate a series of rotated conformations
and only recalculate energies using the 'mdrun -rerun' option.

> 2) In a similar system, I want to include a
> 'crystallographic water' and redo the docking. Does
> Gromacs allow me to use non-SPC water and all-atom FF?

Yes - for example the OPLS forcefield, which is all-atom and uses
tip3p water IIRC is available in Gromacs already. You can simply
add a new topology file for any (most) other types of water model
that you would like to use.

P.S., you should be aware of the Gromacs Users mailing list (I cc
this mail to the list also), for which you can subscribe from the
Gromacs homepage www.gromacs.org
Even without subscribing you can browse and search the list archives.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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