Re: [gmx-users] x2top hangs
Scott Milner wrote: Folks -- I cannot manage to get x2top to work on even the simplest example. Here is "ethane.pdb", a PDB file for ethane (built using Avogadro, with the CONECT records stripped out): COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.2.2b1 ATOM 1 C LIG 1 -3.466 -1.641 -0.001 1.00 0.00 C ATOM 2 C LIG 1 -1.954 -1.689 0.025 1.00 0.00 C ATOM 3 H LIG 1 -3.817 -0.605 0.026 1.00 0.00 H ATOM 4 H LIG 1 -3.882 -2.168 0.863 1.00 0.00 H ATOM 5 H LIG 1 -3.850 -2.112 -0.910 1.00 0.00 H ATOM 6 H LIG 1 -1.570 -1.218 0.934 1.00 0.00 H ATOM 7 H LIG 1 -1.538 -1.163 -0.839 1.00 0.00 H ATOM 8 H LIG 1 -1.603 -2.726 -0.002 1.00 0.00 H END I try to run the following command under GROMACS 4.0, x2top -f ethane.pdb -o ethane.top with the most recent version of the file ffoplsaa.n2t in its proper place (/usr/local/gromacs/share/gromacs/top/), and I get the following output: ... Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t There are 23 name to type translations Generating bonds from distances... atom 0 ... and then the program hangs. Can someone confirm that x2top actually works, and send a simple working example to me? The 4.0.x versions of x2top do not work, as far as I know. The code is undergoing major changes. Version 3.3.3 should be operable, if memory serves. -Justin Scott Milner William H. Joyce Professor The Pennsylvania State University Department of Chemical Engineering 120 Fenske Laboratory University Park, PA 16802 (814) 863-9355 smil...@engr.psu.edu ___ gmx-users mailing listgmx-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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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
[gmx-users] x2top hangs
Folks -- I cannot manage to get x2top to work on even the simplest example. Here is "ethane.pdb", a PDB file for ethane (built using Avogadro, with the CONECT records stripped out): COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.2.2b1 ATOM 1 C LIG 1 -3.466 -1.641 -0.001 1.00 0.00 C ATOM 2 C LIG 1 -1.954 -1.689 0.025 1.00 0.00 C ATOM 3 H LIG 1 -3.817 -0.605 0.026 1.00 0.00 H ATOM 4 H LIG 1 -3.882 -2.168 0.863 1.00 0.00 H ATOM 5 H LIG 1 -3.850 -2.112 -0.910 1.00 0.00 H ATOM 6 H LIG 1 -1.570 -1.218 0.934 1.00 0.00 H ATOM 7 H LIG 1 -1.538 -1.163 -0.839 1.00 0.00 H ATOM 8 H LIG 1 -1.603 -2.726 -0.002 1.00 0.00 H END I try to run the following command under GROMACS 4.0, x2top -f ethane.pdb -o ethane.top with the most recent version of the file ffoplsaa.n2t in its proper place (/usr/local/gromacs/share/gromacs/top/), and I get the following output: ... Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t There are 23 name to type translations Generating bonds from distances... atom 0 ... and then the program hangs. Can someone confirm that x2top actually works, and send a simple working example to me? Scott Milner William H. Joyce Professor The Pennsylvania State University Department of Chemical Engineering 120 Fenske Laboratory University Park, PA 16802 (814) 863-9355 smil...@engr.psu.edu ___ gmx-users mailing listgmx-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
[gmx-users] x2top hangs up
Hello, Trying to generate a topology from PDB file my x2top (gromacs 4.0beta) hangs up. I have the coordinates of carbon nanotube in the PDB file (generated with MOLEKEL). I also have ffencadv.n2t with: C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT double bonded Carbon === ffgmxbon.itp with: [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 x2top -f cnt.pdb -o cnt.top -ff select Then I select "8: Encad all-atom force field, using scaled-down vacuum charges" Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.rtp Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.n2t Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.n2t There are 0 name to type translations Generating bonds from distances... atom 0 And the programme hangs up. The processor load is 99% all the time before I terminate the job. The same data input works with GROMACS 3.3.1 as described by C. Stiles but not with 3.3.3 and 4.0b however. If it is not a bug then what should be modified to make a topology? Has anyone tried to make SWCNT topology in the versions newer that 3.3.1? What essential things have been changed in x2top since 3.3.1? Thanks a lot for suggestions! -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
