When I run
cpptraj -p complex.prmtop -y complex_eq_p.rst -x complex_eq_p.pdb
it gives the information that complex_eq_p.rst file is a NetCDF AMBER
restart file as mentioed below:-
CPPTRAJ: Trajectory Analysis. V17.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 09/04/19 18:22:01
| Available memory: 53.034 GB
Reading 'complex.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
Reading 'complex_eq_p.rst' as Amber NC Restart
Writing 'complex_eq_p.pdb' as PDB
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: complex.prmtop, 68711 atoms, 20735 res, box: Trunc. Oct., 20247 mol,
20237 solvent
INPUT TRAJECTORIES (1 total):
0: 'complex_eq_p.rst' is a NetCDF AMBER restart file, with velocities,
Parm complex.prmtop (Trunc. Oct. box) (reading 1 of 1)
Coordinate processing will occur on 1 frames.
OUTPUT TRAJECTORIES (1 total):
'complex_eq_p.pdb' (1 frames) is a PDB file
BEGIN TRAJECTORY PROCESSING:
Warning: No PDB space group specified.
----- complex_eq_p.rst (1-1, 1) -----
100% Complete.
But how to load it to analyze the box fluctuation for pressure
equilibration.
Thank you
Sadaf
On Wed, Sep 4, 2019 at 6:07 PM Elvis Martis <elvis_bcp.elvismartis.in>
wrote:
> 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
>
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Received on Wed Sep 04 2019 - 10:30:02 PDT
