VMD-L Mailing List
From: maria khan (mariabiochemist1_at_gmail.com)
Date: Sat Jan 14 2017 - 05:11:04 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.