On 10/5/12 5:49 AM, rama david wrote:
Hi Friends,
I want to study the interaction energy between the selected residues of
protein and ligand.
( Non-bonded energy should include : vanderwall and electrostatics)
How to do it???
This is what the energygrps keyword in the .mdp file is for.
Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
How to do it
Would you explain me in detail??
With best wishes and regards,
Rama david.
On Fri, Oct 5, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 5:49 AM, rama david
On 10/5/12 6:15 AM, rama david wrote:
Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
How to do it
Would you explain me in detail??
Create a new .tpr file from an .mdp file with suitable energygrps. Use mdrun
-rerun to recalculate
Hi justin,
thank you for reply.
With best wishes and regards
Rama david.
On Fri, Oct 5, 2012 at 4:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 6:15 AM, rama david wrote:
Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
Hi all,
I want to calculate interaction energy between my ligand and residues of
proetins which come within 6A of any atoms of the raidus. I have defined
those residues and ligand as different groups. But how to select water
around 6A radius of the ligand during dynamicsfor the calculation. If I
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