I checked topology file but going with grompp makes sense. Thank you. On Fri, Jul 9, 2010 at 1:11 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Sai Pooja wrote: > >> Well thats the thing. I have checked my pdb files. All residues have >> > > There aren't charges in a .pdb file, unless you've somehow added them into > one of the fields yourself. The file you need to check is your topology. A > running value of the net charges is given in the [atoms] directive. Charges > are assigned by pdb2gmx based on what is expected in the .rtp file and what > you chose to assign in terms of protonation state. > > > 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 >> > > genbox reads coordinate files, so I don't know how any charge it prints is > meaningful. It tells me there is a zero charge on a lysozyme system that I > know has a +8 charge (regardless of whether or not I pass it a topology as > well), so don't believe genbox. Believe grompp. The magnitude is indeed > due to small rounding errors. It should be interpreted as -1. > > -Justin > > 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<mailto: >> 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 >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> >> > -- > ======================================== > > 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 > -- Quaerendo Invenietis-Seek and you shall discover.
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