[gmx-users] (no subject)

[Francesco Carbone]

I would use -dump to extract only the last frame,
I believe that what your are doing is saving your trajectory in a pdb file.



On 14 May 2016 at 16:21, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> Sure, but if you have a million frames, then you are probably doing
> something other than what you want or should do. See
>
> http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
>
> Mark
>
> On Sat, May 14, 2016 at 5:15 PM Upasana Ray <upasanaray117 at gmail.com>
> wrote:
>
> > I have modelled my protein using homology modeling software & then have
> > used gromacs for energy minimization.
> >
> > gmx trjconv -f md22.xtc -s md22.tpr -o md22.pdb
> > then I have choosen only protein from the options
> >
> > On Sat, May 14, 2016 at 3:55 PM, Pratiti Bhadra <
> pratiti.bhadra at gmail.com>
> > wrote:
> >
> > > How many frames do u save using trjconv?. Can you please post your full
> > > trjconv command here.
> > > On 14 May 2016 18:21, "Chalaoux, Francois-Regis" <
> > > Francois-Regis.Chalaoux at evotec.com> wrote:
> > >
> > > > What is your protein, PDB Id ?
> > > >
> > > > FR.
> > > >
> > > > > Le 14 mai 2016 à 12:04:09, Upasana Ray <upasanaray117 at gmail.com> a
> > > > écrit :
> > > > >
> > > > > yes I have removed water & the pdb file only contains  protein
> > > > >
> > > > > On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis <
> > > > > Francois-Regis.Chalaoux at evotec.com> wrote:
> > > > >
> > > > >> Hi,
> > > > >>
> > > > >> Did you removed Water ?
> > > > >> Check also there is no other protein in the same file.
> > > > >>
> > > > >> FR.
> > > > >>
> > > > >>> Le 14 mai 2016 à 07:04:15, Upasana Ray <upasanaray117 at gmail.com>
> a
> > > > >> écrit :
> > > > >>>
> > > > >>> Dear  user,
> > > > >>>
> > > > >>> I have generated my final protein.pdb file by using trjconv
> command
> > > > from
> > > > >>> .xtc file. The size of my pdb file is 0.98 GB, so whenever I am
> > > opening
> > > > >> it
> > > > >>> for docking purpose my computer is freezing. Now how can I reduce
> > my
> > > > pdb
> > > > >>> file size  from GB to MB for using it properly. please help me to
> > > deal
> > > > >>> with this problem.
> > > > >>> --
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