By what you mentioned in your previous email it seems to me that file
format of the rst you obtained is netcdf.
The output format is controlled by following flags (defaults from amber16
onwards)
Ioutfm = 1 (default) netcdf for trajectory.
ntxo = 2 (default) Netcdf for restrt file.
If you did not define them in you input file then surely your rst file is
in netcdf format
On Wednesday, September 4, 2019, Sadaf Rani <sadafrani6.gmail.com> wrote:
> Hi Elvis and Fabian
> I followed the following tutorial and there is no rst7 file format
> mentioned in commands (however both rst7 and rst files are restart files):-
> http://ambermd.org/tutorials/advanced/tutorial8/loop8.htm
> Now I dont have any netcdf file e.g. .nc file or .rst7 file
> what should I do for the current results as I have following files
> file.prmtop, file.rst, file.crd and file.out
> Please suggest.
>
> thank you
>
> Sadaf
>
>
> On Wed, Sep 4, 2019 at 5:23 PM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > You must select the type of file as netcdf (not amber restrt file) while
> > loading your restrt file in VMD.
> > I am not sure if VMD on windows has started to support netcdf format but
> in
> > Linux you should have no problem.
> >
> > On Wednesday, September 4, 2019, Sadaf Rani <sadafrani6.gmail.com>
> wrote:
> >
> > > Hi Elvis
> > > it is an amber restart file (eq_p.rst as mentioned in below command)
> > > I have selected amber restart file from file format options
> > > The vmd window gives following message
> > > I rst7plugin) Title: CDF
> > >
> > > I am using following command
> > > sander -O -i eq_p.in -p complex.prmtop -c Heat.rst -r eq_p.rst -x
> > > eq_p.crd
> > > -o eq_p.out
> > > I also tried with .crd file but nothing is shown in vmd
> > >
> > > Looking forward to hear from you
> > >
> > > thank you
> > >
> > > Sadaf
> > >
> > > On Wed, Sep 4, 2019 at 4:21 PM Elvis Martis <elvis_bcp.elvismartis.in>
> > > wrote:
> > >
> > > > Are you trying to load netcdf format restart file in VMD?
> > > >
> > > > On Wednesday, September 4, 2019, Sadaf Rani <sadafrani6.gmail.com>
> > > wrote:
> > > >
> > > > > Dear Amber users
> > > > > I have run constant pressure constant temperature equilibration. I
> > want
> > > > to
> > > > > look for the box size for the but when I load .prmtop file in vmd
> and
> > > > load
> > > > > .rst file on it, vmd stops working and vmd window shows that this
> > file
> > > > > could not be read. Could anyone please suggest me which files to
> load
> > > in
> > > > > vmd and analyze box.
> > > > >
> > > > > Thanks in advance.
> > > > >
> > > > > Sadaf
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > > --
> > > > Best Regards
> > > > Elvis Martis
> > > > Mumbai.
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Best Regards
> > Elvis Martis
> > Mumbai.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best Regards
Elvis Martis
Mumbai.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 04 2019 - 10:30:02 PDT
