Fw: Fw: [gmx-users] trjconv in martini

[mohammad agha]

----- Forwarded Message -----
From: mohammad agha <mra_bu at yahoo.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org> 
Sent: Tuesday, January 10, 2012 9:08 PM
Subject: Re: Fw: [gmx-users] trjconv in martini
 

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 exactly?

May I ask you to help me, Please?

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 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
matter.

Good luck,

Tsjerk



-- 
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
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120110/e32114a4/attachment.html>