[gmx-users] Conversion of gromacs trajectory file
Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. Thank you, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Conversion of gromacs trajectory file
aiswarya.pa...@gmail.com wrote: Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. The key is finding a compatible intermediate that can be converted. I've found that PDB format is pretty universal. I have a script that does the opposite (mdcrd to .xtc) linked from my site: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html It's a bit awkward, but does the job. Perhaps you can reverse-engineer it for your purpose. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Conversion of gromacs trajectory file
Hi Justin, Thank for the quick response. I would try out your script for the conversion. Best, Aiswarya --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Discussion list for GROMACS users ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Conversion of gromacs trajectory file Sent: 24 Aug 2011 5:35 PM aiswarya.pa...@gmail.com wrote: Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. The key is finding a compatible intermediate that can be converted. I've found that PDB format is pretty universal. I have a script that does the opposite (mdcrd to .xtc) linked from my site: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html It's a bit awkward, but does the job. Perhaps you can reverse-engineer it for your purpose. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists