[gmx-users] Micelle Modeling

[Justin A. Lemkul]

Janowicz, Adrianna C. wrote:
> Also, I forgot to mention that I need to throw a protein into the mix. How
> would I get both the protein and the DPC into the box?
> 
> 

Have a look through some of the more advanced tutorials.  There is nothing that 
will walk you through all of it explicitly (and it's a LOT to put in an email), 
but you can probably piece it together:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html

Tutorial 2 is probably the most directly applicable.  Instead of a membrane you 
have a micelle, but the principle is the same.

-Justin

> 
> 
> On Tue, July 12, 2011 10:46 am, Justin A. Lemkul wrote:
>>
>> Janowicz, Adrianna C. wrote:
>>> Users,
>>> I'm trying to start a micelle modeling project & have tried countless
>>> approaches to making a DPC micelle. My problems include:
>>> -DPC not being recognized when I try to imput it into the [molecules]
>>> seciton of the topology file to account for the DPC molecules in the
>>> water
>>> topology. Otherwise, the molecule #s do not match. (This approach
>>> included
>>> using a coordinate file for DPC & using the -nmol fuction in genbox to
>>> place the DPC molecules into the water).
>>>
>>> I would appreciate any help. Even if this means taking a totally
>>> different
>>> approach in getting the DPC molecules into the box.
>>>
>> The best approach would be to:
>>
>> 1. Create the topology for a single molecule of DPC
>> 2. Generate a configuration of the DPC micelle and edit the number of
>> molecules
>> in the .top appropriately
>> 3. Solvate and let genbox add the correct number of water molecules to the
>> .top
>>
>> -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

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