[gmx-users] (no subject)

[Upasana Ray]

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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