[gmx-users] protein problems (aka why me?)

David L. Bostick dbostick at physics.unc.edu
Mon Aug 12 17:10:07 CEST 2002

Hi ..

I did exactly (sort of this) when modelling halorhodopsin.  You need to
create a residue in the database.  Jeremy Smith had a few papers a while
back on a model of the retinal moiety.. you may find this a useful guide
for parameters.


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Mon, 12 Aug 2002, J Simms wrote:

> Hi all,
> 	 I am trying to do some MD on a protein called rhodopsin ( a G
> protein coupled receptor with a covalently attached ligand,
> retinal).pdb2gmx doesnt work as the structure contains RET, and
> this is not contained in the .rtp files.Can I use pdb2gmx to get a
> .top file of the protein alone (ie without retinal) and use this as a
> template to work from so that i can use editconf to get a .gro file of
> the complete protein (ie with retinal) and then modify my .top file
> with the .itp file of retinal etc????
> Please no heckling if this is a really dumb idea (Doh!), Any ideas
> wont go amiss either.
>      Many Thanks in Advance
> 	John
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