I guess its the amber03 force field I'm having issues with. The lysozyme tutorial works if I use -ff G43a2 Thanks
Jack On Tue, Mar 17, 2009 at 8:01 PM, Justin A. Lemkul <[email protected]> wrote: > > Well, several tutorials use lysozyme, PDB 1AKI. I would also recommend not > using ffamber if you are running automated tests, since there are quirks > with requiring specific nomenclature (for lysine, histidine, terminal > residues, etc). > > -Justin > > Jack Shultz wrote: >> >> Justin, >> >> Can you suggest any pdb files I could use that are more simple? I've >> been trying to use files from tutorials but it seems like are always >> problematic. >> >> Jack >> >> On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul <[email protected]> wrote: >>> >>> Jack Shultz wrote: >>>> >>>> Hello, >>>> >>>> I just wanted to compare results between single and double precision. >>>> I reused the same parameters. Single works. Double caused errors on >>>> mdrun. Any idea why? >>>> >>>> http://hydrogenathome.org/result.php?resultid=1292662 >>>> >>> I don't know why any of that worked at all. You've got missing atoms and >>> inconsistent naming (LYSH should be LYP if you really want a protonated >>> lysine under the Amber ports, etc). Did you give pdb2gmx -missing? >>> Otherwise, topology generation should have failed. >>> >>> Especially troublesome: >>> >>> System has non-zero total charge: -2.309866e+01 >>> >>> I would suggest running tests on a physically realistic system that has >>> all >>> atoms present and an integer charge. Maybe single precision somehow >>> overcame these topology problems, but I wouldn't trust any of the >>> results. >>> >>> -Justin >>> >>>> ------------------------------------------------------- >>>> Program mdrun, VERSION 4.0.3 >>>> Source code file: nsgrid.c, line: 357 >>>> >>>> Range checking error: >>>> Explanation: During neighborsearching, we assign each particle to a grid >>>> based on its coordinates. If your system contains collisions or >>>> parameter >>>> errors that give particles very high velocities you might end up with >>>> some >>>> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot >>>> put these on a grid, so this is usually where we detect those errors. >>>> Make sure your system is properly energy-minimized and that the >>>> potential >>>> energy seems reasonable before trying again. >>>> >>>> Variable ci has value -2147483648. It should have been within [ 0 .. 300 >>>> ] >>>> >>>> >>>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Graduate Research Assistant >>> 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 list [email protected] >>> 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 >>> >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > 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 list [email protected] > 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 > -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org _______________________________________________ gmx-users mailing list [email protected] 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
