[gmx-users] protein+ligand+membrane: which forcefield?

[vferrario at units.it]

Dear Anna,

I think it's better to keep one single force field... I don't know  
which ff is better for your simulation, but for example you can  
manually correct the definition that PRODRG gives you and adjusting it  
for GROMOS 53a6 paramenters.

Valerio

anna.marabotti at isa.cnr.it ha scritto:

> Dear all,
>
> I have to perform a simulation in which a protein with a ligand is
> included in a lipid bilayer+water. In the Justin Lemkul's tutorial on
> membrane simulations, I see that the chosen forcefield is Gromos96 53a6
> manually corrected to include the Berger lipids parameters. However, to
> create the topology of the ligand, I usually use PRODRG that produces
> the topology and parameters using the Gromos96 43a1 forcefield (it
> should do, at least...I see that the web server has recently changed and
> I don't see the indication of the forcefield used inside...) My
> question is: how to deal with the two different forcefields? I see in
> the gmx-user list that the use of different forcefields is strongly
> discouraged (and I agree with this suggestion) however if I have to
> manage such different systems, what can I do? Can I add the Berger
> lipids parameters to Gromos96 43a1 and use this corrected forcefield
> instead? I did not understand if the Gromos 53a6 ff was chosen in the
> tutorial because it is better than 43a1 to manage such systems, or
> because it is more compliant than 43a1 with Berger lipids parameters.
>
> Many thanks for suggestions and best regards.
>
> Anna Marabotti
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