should i do this ? : i should change dppc from 128lipid (topol_dppc.top) to 6300atom and system_inflated.gro from 6348 t0 6300 ? but why is number of system.gro 6538 ? (6400 + 138) 50 is atom per lipid
On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/15/16 9:26 AM, roshanak starlight wrote: > >> hello . when i want to do energy minimizationin step 3 , with this >> command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o >> em.tpr >> (or confout.gro replace em.tpr) i face with this error: >> >> Fatal error: >> number of coordinates in coordinate file (system_inflated.gro, 6438) >> does not match topology (topol.top, 138) >> >> Earlier, right after this command : perl inflategro.pl system.gro 4 DPPC >> 14 >> system_inflated.gro 5 area.dat >> , i updated [molecules] in topol-dppc.top from 128 to 126 dppc (because of >> this sentence in terminal: >> There are 2 lipids within cut-off range... >> 1 will be removed from the upper leaflet... >> 1 will be removed from the lower leaflet...) >> >> where is the problem from ? >> >> > Apparently you didn't actually update the topology. > > 126 * 50 = 6300 > 6438 - 138 = 6300 > > So your topology specifies no lipids. > > -Justin > > > On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 7/15/16 4:56 AM, roshanak starlight wrote: >>> >>> excuse me i forgot that write subject. >>>> >>>> On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight < >>>> starlight....@gmail.com >>>> >>>> wrote: >>>>> >>>>> >>>> hello >>>> >>>>> i use kalp-15 in dppc tutorial that there is in this website : >>>>> http://www.bevanlab.biochem.vt.edu >>>>> i have 2 question about step 3 : >>>>> 1.after this command : genrestr -f KALP_newbox.gro -o strong_posre.itp >>>>> -fc 100000 100000 100000 which shoud i choose ? ( i choose >>>>> 1:protein . >>>>> is it right ?) >>>>> >>>>> >>>> From the tutorial: >>> >>> "The authors of the InflateGRO script recommend using a very strong >>> position-restraining force on protein heavy atoms to ensure that the >>> position of the protein does not change during EM." >>> >>> So choose the protein heavy atoms (Protein-H). >>> >>> 2.where should i add a line "define = -DSTRONG_POSRES" in minim.mdp ? i >>> >>>> add it (define = -DSTRONG_POSRES ) to end of my file . is it true? >>>>> thank you >>>>> >>>>> >>>>> It doesn't matter. >>> >>> -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. >>> >>> > -- > ================================================== > > 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.
