Fw: [gmx-users] trjconv in martini

[mohammad agha]

Hi Tsjerk, 


Thank you very much from your reply, I think you're right, my problem is about python installation, I take error when I want to install python 2.5 and 2.6, now I am installing the python 2.3. My workflow is according to what you said me means:
# Get a clustered reference frame
trjconv -s md.tpr -f md.trr -o cluster.gro -pbc cluster -dump 200000

# Extract the first part of the trajectory
trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 19999

# Reverse it
./xtcrev.py 1a.xtc > 1a-rev.xtc
and it wasn't ran here, after installation of python I will practice again your workflow. I hope work this time.

I thank you very very much again.

Best Regards
Sara


________________________________
 From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, December 31, 2011 2:18 PM
Subject: Re: Fw: [gmx-users] trjconv in martini
 
Hi Sara,

You do have python installed, don't you? Maybe you have to have
version 2.5 or 2.6 for this to work, although I think it's not using
any features that were not already in 2.3 or 2.4.

Can you post the workflow you're trying now, pasting the exact commands you use?

Cheers,

Tsjerk

On Sat, Dec 31, 2011 at 10:29 AM, mohammad agha <mra_bu at yahoo.com> wrote:
> Hi Tsjerk,
>
> Thanks for your reply, yes, I did this, too! but my problem wasn't solved!
>
> Best Regards
> Sara
>
> ________________________________
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Sent: Saturday, December 31, 2011 11:42 AM
> Subject: Re: Fw: [gmx-users] trjconv in martini
>
> Hi Sara,
>
> Please find the script as attachment. When saved, you have to make it
> executable using
>
> chmod +x xtcrev.py
>
> Then it should work...
>
> Cheers,
>
> Tsjerk
>
> On Sat, Dec 31, 2011 at 5:59 AM, mohammad agha <mra_bu at yahoo.com> wrote:
>> Hi Tsjerk,
>>
>> Thank you for your reply, yes it is #!/usr/bin/env python
>> May I ask you to help me?
>>
>> Best Regards
>> Sara
>>
>> ________________________________
>> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>> To: mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users
>> <gmx-users at gromacs.org>
>> Sent: Friday, December 30, 2011 8:06 PM
>> Subject: Re: Fw: [gmx-users] trjconv in martini
>>
>> Hi Sara,
>> Make sure the first line of the script is:
>> #!/usr/bin/env python
>> Cheers,
>> Tsjerk
>>
>> On Dec 30, 2011 1:25 PM, "mohammad agha" <mra_bu at yahoo.com> wrote:
>>
>> ----- Forwarded Message ----- From: mohammad agha <mra_bu at yahoo.com> To:
>> Tsjerk Wassenaar <tsjerkw at ...
>>
>> --
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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
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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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
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