VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sat Jan 14 2017 - 06:15:12 CST

Please don't re-post the same question. Things remain simple if they are in
one place. Also - re posting will not get you a quicker answer.

*yeah i manage successfuly loading gro file and it opens up in open GL
> window..and for this im using Graphical interface not script*

A gro file and a trajectory file are 2 different things. To be able to
calculate RMSD you need a trajectory. If you conducted a simulation in
Gromacs, you would have obtained a trajectory file. This trajectory file
contains information -- which is basically how the protein moves. Just the
GRO file cannot be used for RMSD calculation.

* can u send me stepwise procedure for the whole analysis *

for RMSD:

step 1) load GRO file
step 2) load trajectory file
step 3) run the following as script

set file_ [open rmsd.vals a]
set nf [molinfo top get numframes]
set ref [atomselect top all frame 0]
for {set i 0} {$i < $nf} {incr i} {

set sel [atomselect top all frame $i]
set mx [measure fit $ref $sel]
$sel move $mx
set rmsd [measure rmsd $ref $sel]
puts $file_ $i\t$rmsd
delete sel
}
close $file_

The above script should create a file called rmsd.vals which will have N
number of rows. Where N is the number of frames in your trajectory.
For each row there will be two columns. First column will hold the frame
number. Second column with hold the RMSD value.

Note: The RMSD value is calculated by comparing each frame in your
trajectory to the frame 0 (which is your starting frame).

for HBONDS look at measure hbond first::
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html. Read it.
Once you understand it : Work out the script below.
What you basically need to figure out is what do you want to measure
hydrogen bonds between and what your criterion for a hydrogen bond is?

step 1) load GRO file
step 2) load trajectory file
step 3) run the following as script

set nf [molinfo top get numframes]
for {set i 0} {$i < $nf} {incr i} {

..try filling this part...

}

Note :: the statement "for {set i 0} {$i < $nf} {incr i}" is a for loop
which iterates over your entire trajectory.
This can take time depending on the size of your trajectory, system,
computing power.

If you can't work out how to populate the code for hbonds, write back (but
just once).

*bt as that is a command base code still we need to visualise the results
> by VMd*

I don't understand what you mean. Do you mean you want to graph out values
of energies to visualize trends ??
You need to use a graphing tool for that (VMD is not a graphing tool - it
generates graphs of a few things where the plugin includes that).
I believe xmgrace comes packaged with gromacs (i think) and you can just
make plots from the command line. You can also save values in a file and
use something like matplotlib or R or whatever you find easy to work with.
Or is it something else you want which I am failing to understand?

*and also i dont know how to evaluate energy by gromacs but it can be
> evaluated by gromacs that is i know..*

yes so please write to the gromacs mailing list. (however you can learn
yourself. Start here:: http://manual.gromacs.org/online/mdp_opt.html)

*you need to exhaustively look at all possible details (non-bonded
> energies) to figure that out----sorry im not getting your this point.*

what I meant here was that you need to understand your system first,
without having an understanding it will not work.
Simply put you need to know what energy/interaction to measure/quantify
first before you measure it.

Hope this helps.

On Sat, Jan 14, 2017 at 11:32 PM, maria khan <mariabiochemist1_at_gmail.com>
wrote:

> 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.
>
> 

-- 
Best,
/A