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