>
> 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
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*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
