Hi,
you could use MMPBSA and designate all the urea as 'ligand' and all the
water as 'receptor'. See the MMPBSA tutorial for that. Since this is not
the script's intended usage, you may have to do some of the calculation
steps by hand...
Kind Regards,
Thomas
On Mon, May 23, 2011 3:19 am, dhilip kumar ramalingam wrote:
> Dear Amber Users,
> I have urea and water in my system and i
> want
> to calculate the interaction energy between urea and water, urea and urea,
> water and water. How to do this in amber?
>
> --
> R.Dhilip kumar
> Computational Biophysics Lab
> Department of Biotechnology
> IIT Madras
> Chennai-600036
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon May 23 2011 - 00:30:03 PDT
