On 3/21/13 7:38 AM, Amit wrote:
Dear Dr. Lemkul,
Many thanks for the reply and suggestion. I
believe doing docking first and then going for simulation is more
relevant as this will lessen the nonspecific interaction. Correct me
if I am wrong. Also I would like to ask one more question. I would
That approach is probably more reasonable.
like to simulate gold nanoparticle and protein together. So how can i
prepare the .pdb and topology file for the nanoparticle as it is
composed of charged atoms? Please let me know.
You need a force field that can handle both protein and gold parameters. None
exist by default in Gromacs, but you can introduce new force fields if needed.
There are many posts about such topics in the list archive, but if you are new
to Gromacs, you should probably invest significant time learning how things work
and how the force fields are organized before you try implementing a custom
force field. Doing so is a rather advanced task and require thorough knowledge
of how everything works.
-Justin
On Thu, Mar 21, 2013 at 4:42 PM, Justin Lemkul [via GROMACS]
<[email protected]> wrote:
On 3/21/13 5:11 AM, Amit wrote:
Dear Gromacs Users,
I am new to gromacs software and
currently in learning phase. Currently, I am facing a big problem. I have
two proteins namely A and B. Wet lab results have shown that both A and B
interacts with each other by co-immunoprecipitation techniques. Is there a
way out to know weather protein A really interacts with B through
simulation? Is it possible to simulate both the proteins together in a
single box without doing docking? Can simulation provide the interacting
regions? I want to incorporate both the proteins together in box without
docking. Please correct me if I am wrong.
Depending on the size of the proteins, doing an unbiased simulation of
protein-protein binding may or may not be feasible. There is a high
probability
of nonspecific interactions, which may or may not be relevant. If you bias
the
simulation towards interacting in some preconceived way, then the simulation
doesn't show much more than the fact that it did what you told it to do.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [hidden email]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [hidden email].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
________________________________
If you reply to this email, your message will be added to the discussion
below:
http://gromacs.5086.n6.nabble.com/Reg-Validation-of-Protein-Protein-Interaction-through-simulation-tp5006514p5006519.html
To unsubscribe from Reg: Validation of Protein-Protein Interaction through
simulation, click here.
NAML
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
