[gmx-users] Micelle Modeling
Justin A. Lemkul
jalemkul at vt.edu
Tue Jul 12 19:47:24 CEST 2011
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:
Tutorial 2 is probably the most directly applicable. Instead of a membrane you
have a micelle, but the principle is the same.
> On Tue, July 12, 2011 10:46 am, Justin A. Lemkul wrote:
>> Janowicz, Adrianna C. wrote:
>>> 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
>>> topology. Otherwise, the molecule #s do not match. (This approach
>>> 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
>>> 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
>> in the .top appropriately
>> 3. Solvate and let genbox add the correct number of water molecules to the
>> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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