in OPLS ff when i use tip3p water i got this error but if tip3p selected then there no problem and it's interesting!
On Mon, Jan 4, 2016 at 2:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/4/16 4:27 AM, soumi wrote: > >> Respected Sir, >> I am new user of gromacs. When I use the following command >> gmx grompp -f ions.mdp -c 1aki_solv.gro -p topol.top -o ions.tpr >> >> I get the following error :Number of coordinates in coordinate file does >> not match topology file. >> Please tell me how can I correct the number of coordinates in gromacs? >> >> > > http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology > > Since you've (presumably) already solvated the system, you probably forgot > to let genbox adjust your topology for you via the -p option. Based on > your file naming, I assume you're following my lysozyme tutorial, which > lays everything out exactly, so be sure you're using the exact commands and > you know what each option is doing. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.