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

[Dallas Warren]

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
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> >>
> >>
> >
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