[gmx-users] Micelle Modeling
Janowicz, Adrianna C.
ajanow3 at uic.edu
Tue Jul 12 19:44:35 CEST 2011
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?
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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