[gmx-users] Protein comparison

[md kashif]

Dear all
 I have protein pdb file and protein+ligand pdb file generated after
docking. How can I compare them by using gromacs? With the word "compare "
I mean that what kind of analysis I can perform? Should I perform binding
energy calculation or rmsd calculation for protein stability change? Kindly
suggest any tutorial for help.

Thanks


On Sun, Nov 16, 2014 at 3:13 PM, md kashif <kashifzamir180.mk at gmail.com>
wrote:

> Dear all
>  I have protein pdb file and protein+ligand pdb file generated after
> docking. How can I compare them by using gromacs?
>
> Thanks
>