VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Jan 13 2017 - 16:41:27 CST

Hi,

Your question doesn't give enough detail for someone to post a solution.
Did you manage to successfully load the gro file and the trajectory file
prior to running your analysis?
How did you run your RMSD analysis? Did you do it using a script ? or the
graphical user interface?
Were any errors reported?

Secondly::

Protein - ligand interaction is a very broad term :: You first need to know
how they interact, then go about quantifying that interaction.
Electrostatics, VDW energies ? if you don't know how they interact then you
need to exhaustively look at all possible details (non-bonded energies) to
figure that out

Binding energy has different methods :: you could do implicit solvent -
like perhaps an approximation like GBSA?? or you can do something better
like thermodynamic integration ?? These are your choices and multiple
methods are present to calculate this.

For energy calculations -- depending on what you want - I believe, in
gromacs, you have to make use of index files with proper system labels to
be able to compute energies between groups. If you want just a global
measure of energies, they should be present in the log file. For details on
energies - as that is an MD thing - which you computed from GROMACS perhaps
you need to go to the GROMACS mailing list??? If you were using NAMD you
could look into "NAMDenergy" or "measure energy". However that is not
advisable since you ran your simulations uses a very different forcefield
so energies should be computed using the same. I am not sure if these
plugins support reading gromacs based parameters, I believe that one should
stay consistent i.e. use NAMD for simulations using CHARMM based
forcefields and then use the same for energy calculations. I think NAMD
can run gromacs based simulations but I am not sure about energies
calculation bit seperately once a trajectory has been created -- but having
said that my knowledge on this subject is far from exhaustive.

For calculating the number of hydrogen bonds you can use the plugin ::
http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/

I believe that GROMACS allows you to calculate most of the energies itself.
Perhaps consulting its manual for energy calculation would be a good place
to start.

On Sat, Jan 14, 2017 at 10:44 AM, maria khan <mariabiochemist1_at_gmail.com>
wrote:

> Dear VMD users,,
> i am a new user of VMD.
> im analysing results of MD simulation done by Gromacs when i want to draw
> the RMSD plot,,it gives an empty result showing no graph curve,,how it can
> be solved..i attached the file that u may understand my problem.
> SEcondly how i can calculate protein ligand interaction?
> how i calculate binding energy?
> How i calculate H-bod ?
> Ptential energy.
> Thanks in advance.
> Maria khan.
> 

-- 
Best,
/A