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

Daan van Aalten vdava at davapc1.bioch.dundee.ac.uk
Wed Oct 6 09:49:24 CEST 2004

Hi Marc-Michael

The trick would be to submit to PRODRG a copy of your PDB file where you
have substituted the fluorine on the phosphorus with something else (say a
carbon). Then, when you have your GROMACS topology, you edit the topology
to change
a) the carbon back to fluorine
b) change the P-C to a P-F bond length
c) (perhaps) change the C/F-P-X bond angle as well
d) edit the partial charges



On Tue, 5 Oct 2004 mmblum at bpc.uni-frankfurt.de wrote:

> 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
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