[gmx-users] Re: FAD force field

Anton Feenstra feenstra at few.vu.nl
Thu Jan 12 09:50:08 CET 2006

Dear Rossen,

Thank you for your interest in my work. Below, I will try to answer your 

Rossen Apostolov wrote:

> I have three questions to you:
> How can I use the dihedrals data to make the itp file?

You alreay spotted the error in the tables: the fourth atom for the 
dihedrals is incorrect (there was a bug in my script for generating the 
table from the topology file...), so that data will not get you 
anywhere. You can, however, simply use the dihedral parameter 
definitions from the .rtp file.

Alternatively, what I have done for another, more recent, project, is to 
use the Gromos 43a1 building blocks for flavin and adenine, and combine 
them to FAD. I've included a tar archive file with all the necessary 
files. You can either include the .itp file directly in your topology, 
or run pdb2gmx in this directory so it uses the entry from 'FF.dat' to 
give you a 'fad' forcefield option.

> Do you think I can use the parameters from the paper for FAD
> along with 53a6 for the protein and spc water?
> (I'll probably have to recheck the adenine part)

I'd not do that. The parameters are for the old 'Gromacs' forcefield. 
You'd be better of by taking my new topology (attached) or building one 
yourself from the 53a6 flavin and adenin blocks (or, modify my 43a1 
version accordingly).

> What lipid is "recommended" for membrane simulation with GROMACS? POPC?

I'm no expert in lipid simulations. Check the work from Peter Tieleman 
(various proteins and protein systems in bilayers) and Siewert-Jan 
Marrink (lipids, mixtures, micelles and bilayers)

P.S., I cc'd this mail to the gromacs mailinglist, which often is the 
best and fastest way to get an answer (from any of the subscribed users) 
for your gromacs questions.



* NOTE: New Affiliation, Phone & Fax numbers (below) *
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
|(   |   )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands  |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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