[gmx-users] Trj conversion: ABCXYZ to AXBYCZ

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 11 16:05:10 CEST 2010 

Hi Nahren,

You probably used make_ndx for making the index file. Unfortunately it sorts
the indices. You have to construct it in such a way that that the indices
are in the order you want them. You can script the generation, based on the
chain ID, or you can make separate index files that you concatenate
together. In the latter case, do mind to remove the index group tags that
are placed at the top of each file and add such a tag at the top of the
concatenated file.

Cheers,

Tsjerk

On Tue, May 11, 2010 at 3:35 PM, nahren manuel <meetnahren at yahoo.com> wrote:

> 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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-- 
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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