excuse me.i don't understand . should i update [molecule] just in *topol.top* ? how? my topol.top file in [molecule] has not any number :
[ molecules ] ; Compound #mols Protein 1 in my topol_dppc.top is this: [ molecules ] ; molecule name nr. DPPC 128 SOL 3655 On Fri, Jul 15, 2016 at 6:12 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/15/16 9:40 AM, roshanak starlight wrote: > >> should i do this ? : >> i should change dppc from 128lipid (topol_dppc.top) to 6300atom and >> > > topol_dppc.top is only ever used for making molecules whole, and never > again. > > system_inflated.gro from 6348 t0 6300 ? >> > > Do not change the .gro file at all. > > but why is number of system.gro 6538 ? (6400 + 138) >> > > In system.gro (and the corresponding topol.top) you have 128 lipids and > the peptide. Then InflateGRO removes two of those lipids, so you have to > account for this in topol.top, which now has the peptide and 126 lipids. > > -Justin > > > 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. >>> >>> > -- > ================================================== > > 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? 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