[gmx-users] Number of Contacts

[Sundari]

Hi,

I used the following command..
gmx mindist -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -od
minidist.xvg -on numb_count  -d  0.65
By doing this I got this numb_count.xvg graph here

https://drive.google.com/open?id=0B99qIEZlZSXfVnQxY3JsUm1rRnc

In this number of contacts varying up to  500 which is impossible for my
 small peptide chain ( two chains in a simulation box and both are seven
residue long ). From this  I concluded that may be number is so high,
because in command line -d 0.65 is not the  COM distance. So than I used
this

gmx select -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -select 'group
"sd-1" and within 0.65 of com of group "sd-2"' -os size.xvg

Where group sd-1 and sd-2 are the side-chain atom index for 1st and 2nd
peptide chain. The output by this command is in below link


 https://drive.google.com/open?id=0B99qIEZlZSXfRDlXN3RaVFROc2s

here, output is a size.xvg file which is looking something feasible. I am
not sure is that output contains number of inter peptide contacts   which I
needed or this is something else as the name suggested "size.xvg". Please
clear my confusion.

Thank you!

Sundari



On Wed, Jun 28, 2017 at 6:55 AM, Dallas Warren <dallas.warren at monash.edu>
wrote:

> First thing you should do when asking for help, is specify exactly
> what you have have done (that includes the command line and output),
> and then why it is "wrong result".
> 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 28 June 2017 at 01:27, Sundari chaudhary <sundi6170 at gmail.com> wrote:
> > Dear all,
> >
> > I want to calculate the number of inter-peptide and intra-peptide
> > side-chain–side-chain contacts and the criteria to form a contact is
> that:
> > the distance between the centers of mass of two residues is less than a
> > specified distance. I tried gmx mindist and gmx distance command lines
> but
> > i got wrong results.
> >
> > Please suggest me right command line to do this analysis.
> >
> >
> > Thank you!
> >
> > Sundari
> > --
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