[gmx-users] protein problems (aka why me?)
JXS818 at bham.ac.uk
Mon Aug 12 17:02:38 CEST 2002
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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