[gmx-users] Trj conversion: ABCXYZ to AXBYCZ

[nahren manuel]

Dear Tsjerk,
The trjconv is not working, it is likely that i am not issuing the proper commands.


--- My ndx file - - -
Select group for output
Group     0 (      System) has  2619 elements
Group     1 (     Protein) has  2619 elements
Group     2 (   Protein-H) has  2619 elements
Group     3 (     C-alpha) has   873 elements
Group     4 (    Backbone) has  2619 elements
Group     5 (   MainChain) has  2619 elements
Group     6 (MainChain+Cb) has  2619 elements
Group     7 ( MainChain+H) has  2619 elements
Group     8 (   SideChain) has     0 elements
Group     9 ( SideChain-H) has     0 elements
Group    10 (r_1-152_r_457-595) has   873 elements
Group    11 (r_153-304_r_596-734) has   873 elements
Group    12 (r_305-456_r_735-873) has   873 elements
Group    13 (     a_1-456) has   456 elements
Group    14 (a_1-456_a_1369-1785) has   873 elements
Group    15 (a_457-912_a_1786-2202) has   873 elements
Group    16 (a_913-1368_a_2203-2619) has   873 elements
Group    17 (a_1-456_a_1369-1785_a_457-912_a_1786-2202_a_913-1368_a_2203-2619) has  2619 elements


Kindly advice
nahren

--- On Mon, 5/10/10, nahren manuel <meetnahren at yahoo.com> wrote:

From: nahren manuel <meetnahren at yahoo.com>
Subject: Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Monday, May 10, 2010, 3:50 PM

Dear Tsjerk,

No the problem was not with GROMACS. I have one structure as a X-ray and the other i created by homology modeling based on this structure. So the difference arose because my starting structures themselves were different.

I did try trjconv with an index file , but it did not work out fine. I will check them once again before getting back.

Thank you

nahren

--- On Mon, 5/10/10, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Monday, May 10, 2010, 3:35 PM

Hi Nahren,

You can
 do that using trjconv and an index file with the atom indices as they are in the order as they have to be.

But is that really your problem? To understand what happened, it would help if you gave the series of commands that led to these results.


Cheers,

Tsjerk

On Mon, May 10, 2010 at 11:42 AM, nahren manuel <meetnahren at yahoo.com> wrote:




	
	
	
	

Dear Gromacs Users,

I simulated
two homologous  (proteins) , and noticed after the simulation that in
one trajectory, the protein is stored as ABCXYZ and in another it is
as AXBYCZ. (where A, Z are chain information, ABC is a trimer and XYZ
is another trimer, so the system is a trimer-trimer complex)



I should not have any issues for most
of my trajectory analysis. But when I wanted to get a correlation
plots of the CA-CA from the covariance matrix, the plots cannot be
compared, as the information in the trajectory is different.



So is there a way that I can convert my
trajectory from ABCXYZ to AXBYCZ. 




Thank you,
nahren



      
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-- 
Tsjerk A. Wassenaar, Ph.D.


post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands


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