Re: AMBER NetCDF file for Simulation

From: Brian Radak (
Date: Wed Jun 06 2018 - 09:12:17 CDT

I believe the recommended extensions for AMBER formats are rst7 and ncrst7
- this should help VMD recognize the proper way to read files.

I'm not entirely clear what you did here. Did you load the prmtop and
restart files and then save as a pdb? When and how did you minimize the

Do you mean "how can I start a simulation in NAMD with NetCDF restart"? To
my knowledge you cannot. It has to be a PDB, an ASCII rst7, or a NAMD
binary coordinate file. I have not tried this personally.

On Wed, Jun 6, 2018 at 8:33 AM, Aashish Bhatt <>

> Dear Sir
> I have problem for starting simulation.I have created biological assembly
> of protein via the help of pymol.Due to bigger size of protein i have
> created topolgy*(file.prmtop)* and*(NetCDF file or binary
> formatted file) *instead of coordinate(*file.inpcrd*) file in amber 17.
> In vmd i have upload and topology>Netcdf>Savecoordinate>*file.pdb*
> and giving path but in minimization system is burst.
> I have 2 question how can i start simulation giving path to the
> file.
> If i used VMD approach (mentioned above) then how can correct this
> simulation.
> Regards
> Aashish Bhatt
> INST-Mohali

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