[gmx-users] Protein comparison

[rama david]

Dear MD,


 You are asking this question again. but let to tell you,
 the energy comparison are made by docking software. Please
see the manual of software and mentioned the name of software you are using.

By gromacs you can do the MD simulation and do analysis of other
interaction pattern.

You cant compare just docking result  in gromacs.




On Mon, Nov 17, 2014 at 9:37 AM, 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? 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
> >
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