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

[Anna Marabotti]

Dear Justin,
thank you very much for your always useful suggestions. I think I will use
the combination of G43a1+Berger in order to overcome the problems of using 3
different forcefields, and I will check carefully the topology created by
PRODRG for the ligand, according to your paper.

Many thanks also to Valerio for his kind suggestion.

Anna
 
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Message: 5
Date: Wed, 02 Feb 2011 12:54:32 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] protein+ligand+membrane: which forcefield?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4D499A58.7000504 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



anna.marabotti at isa.cnr.it wrote:
> 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

The original PRODRG produced topologies designed for use with Gromos87, but 
PRODRG beta includes 43A1:

http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta

Of course, neither is particularly accurate (see the linked paper):

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

> 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.
> 

I have seen both 43A1 and 53A6 used in conjunction with the Berger lipids,
and 
there is no fundamental difference between the two with respect to membrane 
protein systems.  In fact, Berger + Gromos96 is, in and of itself, a
compilation 
of different force fields.  It just happens that they play nicely with one 
another :)

I use 53A6 because it is newer and its derivation is published.  The
information 
for 43A1 is not freely available (i.e., the GROMOS software manual), so I
can't 
decide if I like it or not.  Thus, I generally do not use it.

As for your problem, since the PRODRG charges and charge groups are always 
incorrect (at least, I've never found a molecule it builds properly), you
can 
replace them with whatever you choose.  Since the atom types (for most
atoms) 
are named the same between 43A1 and 53A6, and the bonded parameters are the 
same, you can simply replace all of the charges and charge groups in the
PRODRG 
topology and you will have a 53A6-compatible topology.  Of course, that
implies 
you've derived those charges properly, which is no small task.

-Justin

> Many thanks for suggestions and best regards.
> 
> Anna Marabotti

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================


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