On 1/11/10 4:39 AM, KM wrote:
The parameters for ffgmx have been developed by Christian Kandt. I
have it. I need appropriate data specific for G53a6 which is obviously
lacking. Some atom types changed plus there are G53a6 potentials that
need to be added. I could try to add the lacking data e.g. with the
paper of G53a6 developers, however this is something that should be
done by more experienced users, I believe.
Parameterization is indeed an advanced topic. However, looking at the retinal
structure (in its Schiff base form), it should be rather straightforward to map
atom types and charges to it. The molecule is mostly neutral, with the
exception of the amide, for which parameters exist. The rest of the work is in
the bonded parameters (since the hydrophobic portion of the molecule is also
rather simple, as far as atom types go).
Validation can then be done by the prescribed methodology or some other suitable
alternative. I have generally found that functional groups in the Gromos96
parameter sets are largely transferable between different molecules.
-Justin
Chris
2010/1/11 Justin A. Lemkul<jalem...@vt.edu>:
On 1/10/10 6:16 PM, KM wrote:
Hello,
I would like to simulate bacteriorhodopsin embedded into a membrane. I
think ffG53a6 is a good choice - force field is quite new (at least
newer than ffgmx) and there are topologies available for the most
popular lipids, for example the set developed by Andreas Kukol.
To run a simulation I will need parameters for retinal and Schiff base
connecting Lys216 with retinal. I have those parameters for ffgmx,
however they are incompatible with ffG53a6 (and that's no surprise).
Does anyone know where I can get parameters for ffG53a6 force field
(or compatible with it)?
Chris
If they're not already in the literature or the User Contribution site on
the Gromacs website, you'll likely have to develop them yourself. See, for
example:
http://www.gromacs.org/Documentation/How-tos/Parameterization
I know I have seen several simulations of backteriorhodopsin in the
literature, so perhaps you can find parameters that have already been
published.
-Justin
--
========================================
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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--
========================================
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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