Well thats the thing. I have checked my pdb files. All residues have either 0 or integer net charges. The number 0.9999994 seems like a rounding off error especially since the output of genbox says that the system has zero net charge. Again, I encounter this no-zero net charge when I run grompp with an mdp file for energy minimization with the protein( excluding hydrogen ) restrained.
I am using the charmm implemented version of gromacs. Pooja On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 10/07/2010 1:28 AM, Sai Pooja wrote: > >> >> Hi, >> >> When I start from a energy minimized protein in vacuum and solvate it >> using genbox, the output message says that the protein has zero charge. So I >> skip the genion step. I follow this with energy minimization of the solvated >> protein followed by restraining the protein and then doing a short mdrun (as >> is the usual procedure outlined in most tutorials). However, when I run the >> grompp command as the first step for the position restrained md, it runs but >> prints a note saying that the system has non-zero charge ~ - 0.9999. >> >> NOTE 2 [file finalnoss.top, line 8070]: >> System has non-zero total charge: -9.999994e-01 >> >> I dont understand. Do I need to run the genion step anyway or is it okay >> to continue with this system? >> > > I'd believe grompp before genbox. Surely you know already what is in your > system, and thus its total charge. You should already know the protonation > state of all of your relevant protein residues, because you made choices for > them with pdb2gmx. > > Mark > > > >> Pooja >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> >> >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> > > -- > 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 > -- Quaerendo Invenietis-Seek and you shall discover.
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