VMD-L Mailing List

From: maria khan (mariabiochemist1_at_gmail.com)
Date: Sat Jan 14 2017 - 04:32:11 CST

Thanks alot for your interest ..
yeah i manage successfuly loading gro file and it opens up in open GL
window..and for this im using Graphical interface not script.
one thing is as i have mentiond that im a new user thats why i dont know
how to analyse RMSD and hydrogen bond calculations.can u send me stepwise
procedure for the whole analysis that i may follow it.yes by Gromacs the
energy can be analysed,,bt as that is a command base code still we need to
visualise the results by VMd..and also i dont know how to evaluate energy
by gromacs but it can be evaluated by gromacs that is i know..
And----- by 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----sorry im not getting your this point.
ALso i dont know how to install the plugin that u have referred to me.
THanks once again.

On Sat, Jan 14, 2017 at 10:28 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> HI,
> I would also affirm the suggestion that you do energy evaluations
> using the Gromacs tools rather than mixing values obtained from VMD/NAMD
> with simulations performed with Gromacs. To mix/match a simulation
> computed
> by one with other tools for energy evaluation seems like inviting trouble
> to me. I would hope that most differences would be very minor, but why
> take any risk at all if you don't have to? I would think you would
> want to compute energies using exactly the same force field and
> parameters that were used for the simulation, but that's just my own
> opinion.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, Jan 14, 2017 at 11:41:27AM +1300, Ashar Malik wrote:
> > 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
>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>