Re: [AMBER] how to load amber rst file in vmd for observing box size

From: Sadaf Rani <sadafrani6.gmail.com>
Date: Fri, 6 Sep 2019 20:55:30 +0100

Hi Gustaf and AMBER

I did following:-
 vmd -f [complex.prmtop] -netcdf [complex_eq_p2.rst]
but vmd shows following error:-
ERROR) Unable to determine file type for file '[complex.prmtop]'. Assuming
pdb.
ERROR) Could not read file [complex.prmtop]
ERROR) Loading of startup molecule files aborted.

I did
process_mdout.perl Heat_eq_v.out
it shows that EPOT is becoming stable but it shows data for only 30 steps.
Please find the screenshot attached
Could you please suggest why this only shows for 30 steps only from the
output file completely run till 60000 steps as mentioned below:-

NSTEP = 59500 TIME(PS) = 29.750 TEMP(K) = 296.46 PRESS =
0.0
 Etot = -162697.5847 EKtot = 41669.2354 EPtot =
-204366.8201
 BOND = 1538.1103 ANGLE = 4023.1180 DIHED =
 6504.8927
 1-4 NB = 1817.5173 1-4 EEL = 17582.9827 VDWAALS =
22950.2642
 EELEC = -258783.7053 EHBOND = 0.0000 RESTRAINT =
0.0000
 Ewald error estimate: 0.4978E-04
 ------------------------------------------------------------------------------


 NSTEP = 60000 TIME(PS) = 30.000 TEMP(K) = 298.28 PRESS =
0.0
 Etot = -162356.4058 EKtot = 41925.9694 EPtot =
-204282.3752
 BOND = 1481.2457 ANGLE = 4048.3030 DIHED =
 6540.0761
 1-4 NB = 1817.3426 1-4 EEL = 17637.0645 VDWAALS =
22157.8089
 EELEC = -257964.2161 EHBOND = 0.0000 RESTRAINT =
0.0000
 Ewald error estimate: 0.4223E-04


thanks in advance

Sadaf

On Thu, Sep 5, 2019 at 7:07 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:

> The syntax you are looking for is:
>
> vmd -f [PRMTOP] -netcdf [NCRST]
>
> You have to define if the file is a binary NetCDF file or an amber RST
> file -rst7. you can use type for this:
>
> type rst-file.xx
>
> If you get a “data-file”, as in:
>
> rst-file.xx data
>
> Then you got yourself a NetCDF file (or some other binary format, however
> in this case it should be a NetCDF file). If it is a text file (ASCII or
> “old” amber7 RST) then you define this as:
>
> vmd -f [PRMTOP] -rst7 [NCRST]
>
> If you just want to se the box dimension fluctuations, I would recommend
> “process_mdout.perl” which is included in amber. Use it as follows:
>
> process_mdout.perl /PATH/TO/simulation.out
>
> Where “out” is the out file for your pressure equilibration or nPT
> simulation. If you have multiple steps, use:
>
> process_mdout.perl /PATH/TO/nPT_step1.out /PATH/TO/nPT_step2.out
> /PATH/TO/nPT_step3.out
>
> You want to do this in a separate directory as you get plenty of output
> files, these files can then bli inspected visually or preferably with
> xmgrace (or gnuplot or prism or some sort of graphing software). By
> choosing which “summary.XXX” file you inspect you can plot fluctuations in
> energy, pressure, temperature and much more as a function of time.
>
> Best regards
> // Gustaf
>
> > On 4 Sep 2019, at 19:25, Sadaf Rani <sadafrani6.gmail.com> wrote:
> >
> > 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
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>


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Energy_EPOT.png
(image/png attachment: Energy_EPOT.png)

Received on Fri Sep 06 2019 - 13:00:03 PDT
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