[gmx-users] Retinal and Schiff base parameters for ffG53a6

[Justin A. Lemkul]

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<jalemkul at 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

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