[gmx-users] Error in system_inflate.gro coordinates does not match
RINU KHATTRI
nickname.mittu at gmail.com
Wed Jul 16 12:53:40 CEST 2014
hello gromacs users
i am working on protein complex with popc membrane
at the time of minimization and shrinking steps my protein complex is out
of the lipid membrane protein is in the lipid membrane till inflate.gro but
after that it is out
i used the minimization script
; minim.mdp - used as input into grompp to generate confout.tpr
"define = -DSTRONG_POSRES"
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0 ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to
perform
energygrps = Protein UNK ; Which energy group(s) to write to
nstlist = 1 ; Frequency to update the neighbor list and
long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple,
grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range
forces)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions
help
On Wed, Jul 16, 2014 at 11:11 AM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:
> 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
>> > >>>
>> > >>> ==================================================
>> > >>> --
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>> > >>
>> > >>
>> > >
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