Justin, Thanks. The problem was that I didn't use "-nopbc" option.
Vitaly On Sun, Jan 17, 2010 at 7:11 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Vitaly V. Chaban wrote: >> >> And more. What is the algorithm to detect that the proper atom group? >> Is it based both on the atom names in PDB and interatomic distances? >> >> So if we have for example >> O opls_236 -0.5 15.9994 1 C 0.123 >> >> and in the submitted structure r(C-O)=0.126 - what it be recognized? >> > > Details are on the Gromacs wiki: > > http://www.gromacs.org/Documentation/Gromacs_Utilities/x2top > http://www.gromacs.org/Documentation/File_Formats/.n2t_File > > If the above doesn't address the original problem (the program hanging), > please post your actual command line. > > -Justin > >> Thanks in advance. >> >> >> ---------- Forwarded message ---------- >> From: Vitaly V. Chaban <vvcha...@gmail.com> >> Date: Sun, Jan 17, 2010 at 6:27 PM >> Subject: x2top(4.0.7) >> To: gmx-users@gromacs.org >> >> >> Hi all, >> >> What can be the reason that x2top(4.0.7) stops with >> >> Looking whether force field files exist >> Opening library file /root/gromacs.407/share/gromacs/top/ffG53a6.rtp >> Opening library file /root/gromacs.407/share/gromacs/top/ffG53a6.n2t >> Opening library file /root/gromacs.407/share/gromacs/top/ffG53a6.n2t >> There are 0 name to type translations >> Generating bonds from distances... >> atom 0 >> >> Meanwhile the processor load is high at that moment and the utility >> never finishes itself. >> >> -- >> Vitaly V. Chaban, Ph.D. >> http://www-rmn.univer.kharkov.ua/chaban.html > > -- > ======================================== > > 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
