[gmx-users] Channelrhodopsin topology

[vicolls at fizyka.umk.pl]

Hello everyone,

I got some troubles with topology setup for channelrhodopsin setup in  
membrane.  It is first such difficult system I met at my short  
scientific way and in fact it blocks my progress. I am not sure if  
gromacs mailing list is the way I should  call for help, but perhaps I  
will find some answers here.

Channelrhodopsin consists of protein, ligand (retinal) bounded to  
protein and there should be membrane. I want to make simulations in  
charmm ff.  I found nice topology created by prof. Jochen Hub, but  
unfortunatly  it is in amber ff.

I have attached protein  to membrane via charmm-gui, but I  had to cut  
off the retinal  (charmm  gui couldn't handle ligand conected to  
protein). So I get nice structure and topology  for both  protein  and  
membrane. Later I wanted to add retinal to  the system - I made it  
manually, by coppying coordinates to gro file and getting topology to   
retinal from swiss-param.

There are two  problems - one is retinal and protein  lives on their  
own. They do't see each other. On tail of retinal and tail of Lys296  
(to which retinal is connected) there are too many hydrgens instead of  
bond. I just deleted it manually, but still I don't have parameters  
for this particular atoms. I don't know where to find them, how to get  
them.

Also I have some mess in  topology, beacuse some parts come from  
charmm-gui and retinal from swiss param. Any ideas how to make nice  
and managable topology files? And how should I connect retinal with  
lys296?

With best regards,
Wiktor