[gmx-users] Md with a ligand containing a P-F bond?

[mmblum at bpc.uni-frankfurt.de]

Hey,

I successfully finished an MD run with a ligand bound to the protein I work
with. The starting structure came from an X-ray structure and I was able to
construct the ligand using the PRODRG server.

I now have a ligand where the starting structure originates from a docking run
with AUTODOCK. The problem is that the ligand (a pesticide) contains a
phosphorous fluorine bond. For this I can not use PRODRG. Is there any
possiblity to generate the topology? If there is I way I would be very thankful
if you could provide me with the basic steps I have to follow.

Thank You for your time and help!

Yours

Marc-Michael Blum

Institute of Biopyhsical Chemistry
University of Frankfurt
Germany