Just to tick all the boxes here, -parm7 seems to be the VMD flag for prmtop files, hence;
vmd -f -parm7 [prmtop] -netcdf [netcdf]
// Gustaf
> On 7 Sep 2019, at 10:14, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> VMD is supposed to recognize prmtop automatically, this might be an indication of a problem with your files. Try preceeding the prmtop with -prmtop or -parm (I don't know the syntax for filetype prmtop, try searching for it) that should load the file if it is not damaged.
>
> Grace (at least mine) converts iterations to [some prefix]seconds, usually nanoseconds. If this is an nPT equillibration you have 6000 iterations, what is your time step (dt) and write out frequency to [out]
>
> Best regards
> // Gustaf
> ________________________________
> Från: Sadaf Rani <sadafrani6.gmail.com>
> Skickat: den 6 september 2019 21:55:30
> Till: AMBER Mailing List
> Ämne: Re: [AMBER] how to load amber rst file in vmd for observing box size
>
> 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
>>>>
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>>> AMBER mailing list
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>>
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Received on Mon Sep 09 2019 - 07:00:02 PDT
