[gmx-users] inactive - active conversion

[J Simms]

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