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

[Anton Feenstra]

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.

1) use prodrg to make molecule without the P and/or F atom(s).
2) add the missing atom(s), you'll have to decide which atomtype and which
    charge to assign.
3) add bonds, angles, possibly proper and improper dihedrals, and exclusions.
    Again, decide which parameters to use for each.

I've put a tar file with some useful scripts on the contributions page.
The one you may find most useful for your purpose is 'renumtop'. Using that,
you can add (in above steps) an atom and number it for example '5b', and
then define the interactions using the '5b' atom number (for a bond, e.g,
beteen atoms 5 and 5b, and an angle between 4, 5 and 5b. Then, use renumtop
to re-assign all atomnumbers (so, 5b will become 6, 6 will become 7 etc.)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|