[gmx-users] inactive - active conversion

[Daan Virtual]

Dear John

I think what you are asking is how you can create a starting model for the
all trans retinal? There are a few ways of doing this.

a) there are structures with all-trans retinal (or retinol) in the PDB,
   get those and either rename the atoms if that's required or re-run
   through PRODRG

b) PRODRG generates topologies for WHAT IF and O - both these programs
   will then allow you to rotate around defined torsion angles in the
   molecule.

goo dluck

Daan




On Sun, 16 Mar 2003, J Simms wrote:

> Hi all,
> I am having trouble converting a ligand from the inactive state (11-
> cis retinal ) to the active state (all trans retinal). I have used
> PRODRG to get the topologies which I have introduced in to the
> .rtp file. My problem is that I am working with a crystal structure of
> Rhodopsin which contains the inactive 11-cis retinal. I run an MD
> sim on the rhodopsin in a DPPC bilayer & all is fine rhodopsin &
> the 11-cis retinal relaxes. I have the topology for the all trans retinal
> (active form) how do I convert the 11-cis retinal to all trans retinal.
> Cheers, as usual any help will be gratefully accepted.
> John
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Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
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