[gmx-users] Error in system_inflate.gro coordinates does not match

RINU KHATTRI nickname.mittu at gmail.com
Wed Jul 16 07:41:06 CEST 2014


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.Warren at 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.warren at 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-bounces at maillist.sys.kth.se
> > [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> > RINU KHATTRI
> > Sent: Wednesday, 16 July 2014 3:24 PM
> > To: gmx-users at 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.mittu at 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.mittu at 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 <jalemkul at 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
> > >>>
> > >>> jalemkul at 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-request at 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-request at 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-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list