anna.marabo...@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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