<html><body><div style="color:#000; background-color:#fff; font-family:bookman old style, new york, times, serif;font-size:14pt"><div><span>Hi Tsjerk, <br></span></div><div><br><span></span></div><div><span>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:</span></div><div># Get a clustered reference frame<br>trjconv -s md.tpr -f md.trr -o cluster.gro -pbc cluster -dump 200000<br><br># Extract the first part of the trajectory<br>trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 19999<br><br># Reverse it<br>./xtcrev.py 1a.xtc > 1a-rev.xtc</div><div>and it wasn't ran here, after installation of python I will practice again your workflow. I hope work this time.</div><div><br></div><div>I thank you very very much again.</div><div><br></div><div>Best
Regards</div><div>Sara<br></div> <div style="font-family: bookman old style, new york, times, serif; font-size: 14pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Tsjerk Wassenaar <tsjerkw@gmail.com><br> <b><span style="font-weight: bold;">To:</span></b> mohammad agha <mra_bu@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, December 31, 2011 2:18 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: Fw: [gmx-users] trjconv in martini<br> </font> <br>
Hi Sara,<br><br>You do have python installed, don't you? Maybe you have to have<br>version 2.5 or 2.6 for this to work, although I think it's not using<br>any features that were not already in 2.3 or 2.4.<br><br>Can you post the workflow you're trying now, pasting the exact commands you use?<br><br>Cheers,<br><br>Tsjerk<br><br>On Sat, Dec 31, 2011 at 10:29 AM, mohammad agha <<a ymailto="mailto:mra_bu@yahoo.com" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>> wrote:<br>> Hi Tsjerk,<br>><br>> Thanks for your reply, yes, I did this, too! but my problem wasn't solved!<br>><br>> Best Regards<br>> Sara<br>><br>> ________________________________<br>> From: Tsjerk Wassenaar <<a ymailto="mailto:tsjerkw@gmail.com" href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>> To: mohammad agha <<a ymailto="mailto:mra_bu@yahoo.com" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>>; Discussion list for GROMACS
users<br>> <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Sent: Saturday, December 31, 2011 11:42 AM<br>> Subject: Re: Fw: [gmx-users] trjconv in martini<br>><br>> Hi Sara,<br>><br>> Please find the script as attachment. When saved, you have to make it<br>> executable using<br>><br>> chmod +x <a target="_blank" href="http://xtcrev.py">xtcrev.py</a><br>><br>> Then it should work...<br>><br>> Cheers,<br>><br>> Tsjerk<br>><br>> On Sat, Dec 31, 2011 at 5:59 AM, mohammad agha <<a ymailto="mailto:mra_bu@yahoo.com" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>> wrote:<br>>> Hi Tsjerk,<br>>><br>>> Thank you for your reply, yes it is #!/usr/bin/env python<br>>> May I ask you to help me?<br>>><br>>> Best Regards<br>>> Sara<br>>><br>>>
________________________________<br>>> From: Tsjerk Wassenaar <<a ymailto="mailto:tsjerkw@gmail.com" href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>>> To: mohammad agha <<a ymailto="mailto:mra_bu@yahoo.com" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>>; Discussion list for GROMACS users<br>>> <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>> Sent: Friday, December 30, 2011 8:06 PM<br>>> Subject: Re: Fw: [gmx-users] trjconv in martini<br>>><br>>> Hi Sara,<br>>> Make sure the first line of the script is:<br>>> #!/usr/bin/env python<br>>> Cheers,<br>>> Tsjerk<br>>><br>>> On Dec 30, 2011 1:25 PM, "mohammad agha" <<a ymailto="mailto:mra_bu@yahoo.com" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>> wrote:<br>>><br>>> ----- Forwarded Message ----- From: mohammad
agha <<a ymailto="mailto:mra_bu@yahoo.com" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>> To:<br>>> Tsjerk Wassenaar <tsjerkw@...<br>>><br>>> --<br>>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>>> Please search the archive at<br>>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>>> Please don't post (un)subscribe requests to the list. Use the<br>>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>>> Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists<br>>><br>>><br>>><br>>><br>>> --<br>>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>>> Please search the archive at<br>>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>>> Please don't post (un)subscribe requests to the list. Use the<br>>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>><br>><br>><br>> --<br>> Tsjerk A. Wassenaar, Ph.D.<br>><br>> post-doctoral researcher<br>> Molecular Dynamics Group<br>> * Groningen Institute for Biomolecular Research and Biotechnology<br>> * Zernike Institute for Advanced Materials<br>> University of Groningen<br>> The Netherlands<br>><br>><br>><br>> --<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the
list. Use the<br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br><br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br><br><br> </div> </div> </div></body></html>