Hi,
VMD detects file format by file name extension, and I don't think
'.rst' is recognized as "Amber restart" by VMD. Try changing the file
name extensions to '.rst7' and see if that helps.
Alternatively, try writing the files in the netcdf restart file format
(.ncrst extension).
-Dan
On Sun, Jan 10, 2021 at 9:41 AM 辛志宏 <xzhfood.njau.edu.cn> wrote:
>
> Dear Amber,
>
>
> I want to extract the 20 rst structures from the nc files using the following script (re_image-480-500-2.in), the rst file generated sucessfully, but the rst file can not be displayed by vmd.
> The top and nc file works in the VMD.
> How to fix the issue?
>
>
> I will be appreciate very much if there are any sugesstion.
>
>
>
>
> The re_image-480-500-2.in file is as follows:
>
>
> parm EstYZ5-DMP-complex-wat.top
> trajin EstYZ5-DMP-wat_equil_reimaged.nc
> trajout EstYZ5-DMP-wat_equil-480.rst restart remdtraj onlyframes 480
> trajout EstYZ5-DMP-wat_equil-481.rst restart remdtraj onlyframes 481
> trajout EstYZ5-DMP-wat_equil-482.rst restart remdtraj onlyframes 482
> trajout EstYZ5-DMP-wat_equil-483.rst restart remdtraj onlyframes 483
> trajout EstYZ5-DMP-wat_equil-484.rst restart remdtraj onlyframes 484
> trajout EstYZ5-DMP-wat_equil-485.rst restart remdtraj onlyframes 485
> trajout EstYZ5-DMP-wat_equil-486.rst restart remdtraj onlyframes 486
> trajout EstYZ5-DMP-wat_equil-487.rst restart remdtraj onlyframes 487
> trajout EstYZ5-DMP-wat_equil-488.rst restart remdtraj onlyframes 488
> trajout EstYZ5-DMP-wat_equil-489.rst restart remdtraj onlyframes 489
> trajout EstYZ5-DMP-wat_equil-490.rst restart remdtraj onlyframes 490
> trajout EstYZ5-DMP-wat_equil-491.rst restart remdtraj onlyframes 491
> trajout EstYZ5-DMP-wat_equil-492.rst restart remdtraj onlyframes 492
> trajout EstYZ5-DMP-wat_equil-493.rst restart remdtraj onlyframes 493
> trajout EstYZ5-DMP-wat_equil-494.rst restart remdtraj onlyframes 494
> trajout EstYZ5-DMP-wat_equil-495.rst restart remdtraj onlyframes 495
> trajout EstYZ5-DMP-wat_equil-496.rst restart remdtraj onlyframes 496
> trajout EstYZ5-DMP-wat_equil-497.rst restart remdtraj onlyframes 497
> trajout EstYZ5-DMP-wat_equil-498.rst restart remdtraj onlyframes 498
> trajout EstYZ5-DMP-wat_equil-499.rst restart remdtraj onlyframes 499
> trajout EstYZ5-DMP-wat_equil-500.rst restart remdtraj onlyframes 500
> run
> quit
>
>
> cpptraj -i re_image-480-500-2.in
>
>
> open one of the rst file by VMD, and the structures cannot be displayed.
>
>
> vmd -parm7 EstYZ5-DMP-complex-wat.top -rst EstYZ5-DMP-wat_equil-480.rst
>
>
>
>
> Zhihong XIN
>
>
> College of Food Science and Technology
> Nanjing Agricultural University
>
>
>
>
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Received on Mon Jan 11 2021 - 10:00:04 PST
