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

J Simms JXS818 at bham.ac.uk
Mon Aug 12 17:02:38 CEST 2002

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

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