[gmx-users] Number of Contacts

[Sundari]

If anyone have Idea.
 kindly suggest.


On Wednesday, June 28, 2017, Sundari <sundi6170 at gmail.com> wrote:

> 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
> <javascript:_e(%7B%7D,'cvml','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
>> <javascript:_e(%7B%7D,'cvml','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
>> <javascript:_e(%7B%7D,'cvml','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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