Re: [gmx-users] Number of Contacts

[Sundari]

If anyone have Idea.
 kindly suggest.


On Wednesday, June 28, 2017, Sundari  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  > 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.war...@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 > > 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
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org
>> .
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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>> .
>
>
>
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Re: [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 
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.war...@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  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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Number of Contacts

[Dallas Warren]

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.war...@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  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
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.
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[gmx-users] Number of Contacts

[Sundari chaudhary]

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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[gmx-users] Number of contacts matrix

[Raphael]

Hi,

could any body help me to plot a N x N matrix (N = number of residues)? But
instead of getting a mean distance matrix (with g_mdmat) for all residues
during a trajectory, I would like to plot a matrix for the number of
contacts (z-axis) within a defined cutoff made by all pairs of residues
(CA).

I was looking for an easy way to do this but I couldn't find it.

Thanks for any help

Raphael

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