[gmx-users] gmx distance

[Dallas Warren]

Documentation on how to use the selections can be found at
http://manual.gromacs.org/current/onlinehelp/selections.html

What you will need here is something to uniquely identify each of the
residues (and atoms?) in the two proteins.

Run the script just on a coordinate file when working out what the correct
syntax is, then compare the distance value it comes up with against what
you find if you measure it by hand using vmd or pymol. This is to ensure
you are defining the selection correctly.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Sat, 9 Mar 2019 at 19:59, marzieh gharouni <gharouni.m2000 at gmail.com>
wrote:

> Hello Dear All
> I did a simulation of protein-protein interaction. I want to obtain a
> distance residue between the two proteins. In the Gromacs tutorial has been
> said to calculate of distance for protein-ligand whereas I want to
> calculate of distance for protein-protein.
> The command of protein-ligand in the Gromacs tutorial:
> gmx distance -s md_0_10.tpr -f md_0_10_center.xtc -select 'resname "JZ4"
> and name OAB plus resid 102 and name OE1' -oall
> can I use resid instead of resname for protein because I have two proteins?
> I would be grateful if you could say command of distance for residues
> between two proteins.
> Thank's a lot.
> --
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