I donot know is amber can do this.
I think you can use PAICS to do it.
PAICS is a program of quantum chemical calculation, which has been
develooped and administrated by Takeshi Ishikawa
<
http://www.paics.net/ishi_e.html>. In this program, fragment molecular
orbital (FMO) method is adopted, by which large molecules including
biomolecular systems can be treated with several quantum chemical
aproaches. At the same time, PaicsView
<
http://www.paics.net/paics_view_e.html> has been developed, which is a
supporting program for using PAICS.
The following site show a theoretical study with the FMO method for the
interaction between prion protein and a small molecule, GN8, which is a
curative agent discovered in our laboratory.
http://www.paics.net/example01_e.html
I hope this program can help you.
Jacky B. Ma
On Wed, Mar 4, 2015 at 2:04 PM, danieldefoe <daniel.defoe.cadd.outlook.com>
wrote:
> Dear all, Could we use Amber to calculate interaction energy between
> any two residues of one protein? I tried with this command:
> MMPBSA -i filename.in -d filename.dat -do filename2.dat -sp
> complex_solvated.prmtop -cp complex.prmtop -x
> filename.mdcrd Is this correct? Best wishes, Daniel defoe
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Mar 03 2015 - 21:30:03 PST
