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
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