Fw: [gmx-users] trjconv in martini
mra_bu at yahoo.com
Wed Jan 11 11:05:39 CET 2012
Thank you very much from your reply. Yes, you're right, I corrected that, but now it gave me this error:
Traceback (most recent call last):
File "./xtcrev.py", line 68, in <module>
o = open(sys.argv,"w")
IndexError: list index out of range
May I ask you to help me, please?
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: Wednesday, January 11, 2012 12:54 PM
Subject: Re: Fw: [gmx-users] trjconv in martini
That can only happen if the input file is empty.
But I now see that the output file should be given as second argument,
so it should be
./xtcrev.py input.xtc output.xtc
./xtcrev.py input.xtc > output.xtc
The latter will actually result in an empty xtc file. Maybe that's the
cause of the problem? Sorry about that.
On Tue, Jan 10, 2012 at 6:38 PM, mohammad agha <mra_bu at yahoo.com> wrote:
> Hi Tsjerk,
> I know that my question is silly but please help me.
> I installed python2.5 on my system, then I ran "./xtcrev.py 1a.xtc >
> 1a-rev.xtc" but it gave me following error:
> Traceback (most recent call last):
> File "./xtcrev.py", line 54, in <module>
> n = 92 + i(f.read(84)[-4:]) # Size of frame in bytes
> File "./xtcrev.py", line 24, in i
> def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)])
> IndexError: string index out of range
> I know that j is out of range but I don't know that what should I do
> May I ask you to help me, Please?
> Best Regards
> 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 3:41 PM
> Subject: Re: Fw: [gmx-users] trjconv in martini
> Hi Sara,
>> # Extract the first part of the trajectory
>> trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 19999
> That should be -e 199999 :) But you can also use -e 200000. Probably
> that is better. I first thought it'd be better to avoid a double
> frame, but since trjcat is used to combine the parts again, it doesn't
> Good luck,
> 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.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
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