hello every one i saw it in vmd representation ->periodic but still protein is out
On Wed, Jul 16, 2014 at 11:01 AM, Dallas Warren <dallas.war...@monash.edu> wrote: > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > Switch on periodic image in VMD and you will that it is not a problem at > all. > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > -----Original Message----- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > > RINU KHATTRI > > Sent: Wednesday, 16 July 2014 3:24 PM > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Error in system_inflate.gro coordinates does > > not match > > > > hello gromacs users > > i saw in vmd system.gro its little bit ok very small fragment of > > protein > > is out but in shrinkage.gro file box and protein is separated > > > > ; Include Position restraint file > > #ifdef POSRES > > #include "posre.itp" > > #endif > > ; Strong position restraints for InflateGRO > > #ifdef STRONG_POSRES > > #include "strong_posre.itp" > > #endif > > > > ; Include ligand topology > > #include "drag.itp" > > > > ; Include POPC chain topology > > #include "popc.itp" > > > > ; Include water topology > > #include "gromos53a6_lipid.ff/spc.itp" > > my topology file > > kindly help > > thanks in advance > > > > > > On Wed, Jul 16, 2014 at 10:20 AM, RINU KHATTRI > > <nickname.mi...@gmail.com> > > wrote: > > > > > hello every one > > > i am working on complex with popc membrane after visualization of > > minimize > > > structure (after solvation and addition of ions 14 cl-) in VMD i saw > > > protein is moving out em.gro from the lipid membrane i dont know how > > to > > > resolve it > > > > > > help > > > > > > > > > On Tue, Jul 15, 2014 at 3:42 PM, RINU KHATTRI > > <nickname.mi...@gmail.com> > > > wrote: > > > > > >> hello everyone > > >> now i got the minimize structure after addition of water and ions > > (14 cl-) > > >> i have been select the > > >> > > >> genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA - > > nname CL -nn 14 > > >> > > >> 13 th option sol in out put > > >> > > >> how can i analyze my structure means is it ok or not because next > > step is equilibration > > >> > > >> kindly help > > >> > > >> > > >> > > >> On Sat, Jul 12, 2014 at 2:48 AM, Justin Lemkul <jalem...@vt.edu> > > wrote: > > >> > > >>> > > >>> > > >>> On 7/11/14, 3:18 AM, RINU KHATTRI wrote: > > >>> > > >>>> hello > > >>>> i am following the lysozyme tutorial > > >>>> > > >>>> editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron -d > > 1.0 > > >>>> > > >>> > > >>> Don't alter the box like this; it's totally nonsensical. > > >>> > > >>> > > >>> solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro > > >>>> > > >>>> but after running second command i got error solvate command > > not > > >>>> found > > >>>> > > >>>> gmx solvate is also not working > > >>>> > > >>>> > > >>> The tutorial corresponds to version 5.0; if you're using an older > > >>> version, the command is called "genbox." > > >>> > > >>> > > >>> -Justin > > >>> > > >>> -- > > >>> ================================================== > > >>> > > >>> Justin A. Lemkul, Ph.D. > > >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow > > >>> > > >>> Department of Pharmaceutical Sciences > > >>> School of Pharmacy > > >>> Health Sciences Facility II, Room 601 > > >>> 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. > -- > 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.