[gmx-users] multi file input for index files

[Tsjerk Wassenaar]

Hey,

In cases where you do end up with two index files, like resulting from
a script or so, you can also simply combine them by concatenation:

cat A.ndx B.ndx > C.ndx

Of course you'll have to make sure that the group names are unique ;)

Cheers,

Tsjerk

2012/1/10 ahmet yıldırım <ahmedo047 at gmail.com>:
> Thanks Mark and Marzinek,
>
> The Problem is solved:
>
> g_hbond -f traj.xtc -s run.tpr -num AB.xvg -n AB.ndx
>
>> chain A
>
> Found 1234 atoms with chain identifier A
>
>  19 chA                 :  1234 atoms
>
>> name 19 chainA
>
>
>> chain B
>
> Found 1234 atoms with chain identifier B
>
>  20 chB                 :  1234 atoms
>
>> name 20 chainB
>
>
>> q
>
>
> 2012/1/10 Marzinek, Jan <j.marzinek10 at imperial.ac.uk>
>>
>> So as you can see Gromacs does not support multi file input :) Create one
>> index file and specify there your two groups. Then g_hbond will ask you to
>> choose two groups from this file.
>>
>>
>>
>> Jan
>>
>>
>>
>>
>> ===========================================================
>> Jan Marzinek
>> PhD Candidate
>> Centre for Process Systems Engineering
>> Department of Chemical Engineering
>> Imperial College London
>> South Kensington Campus
>> London SW7 2AZ
>> E: j.marzinek10 at imperial.ac.uk
>> M: +44(0)7411 640 552
>> ________________________________
>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
>> behalf of ahmet yıldırım [ahmedo047 at gmail.com]
>> Sent: Tuesday, January 10, 2012 8:13 AM
>> To: Discussion list for GROMACS users
>> Subject: [gmx-users] multi file input for index files
>>
>> Dear users,
>>
>> I created two different index files (A.ndx and B.ndx). I want to run the
>> two files at the same time.
>> e.g.
>> g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx
>> where, I want to calculate the hydrogen bonds between A and B.
>> This command is giving the error as it expected. "Gromacs tools do not
>> support multi file input for index files" from
>> http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html.
>> Is this correct? If no, what should I do?
>>
>> Thanks in advance
>> --
>> Ahmet Yıldırım
>>
>>
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>
>
>
> --
> Ahmet Yıldırım
>
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

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