[AMBER] vdw energy and electrostatic energy calculation for osmolyte

From: MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
Date: Thu, 26 Mar 2015 11:29:40 +0530

>
> On Tue, Mar 24, 2015 at 3:31 AM, Subrata Paul <paul.subrata34.gmail.com>

wrote:

> Dear

> Amber User,

>

> I have simulated a protein-urea-water system in AMBER12. Can we calculate

> the vdw energy and electrostatic energy for water and urea around the

> protein separately?

> any hints ?

>

You can strip out the water using cpptraj and
*compute the energy of each​ ​snapshot (using sander with imin=5).*

​Please elaborate this part how we are going to proceed this ? Similar to
the normal MD (trajectory as input instead of rst file ) or any other step
involves. ​

 This will represent the urea-urea,

protein-protein, and protein-urea interactions. Then strip out the urea

and compute the energy of each snapshot. This will represent the

water-water, protein-protein, and protein-water interactions.


​Thanks
Regards
Rahman​

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*Md Homaidur Rahman*
PhD Research Scholar
Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036
*Mobile No = +91- 7845991785*
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Received on Wed Mar 25 2015 - 23:00:03 PDT
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