Re: AMBER NetCDF file for Simulation

From: Aashish Bhatt (aashish.ph16221_at_inst.ac.in)
Date: Thu Jun 07 2018 - 02:02:31 CDT

Dear Brian Radak

>> *AMBER formats are rst7 and ncrst7 >> *
I know this format. When i upload the rst7 and ncrst7 in VMD toplogy or
structure is not correct.
When I upload rst7 and *.nc.rc *structure is perfect.

>>D*id you load the prmtop and restart files and then save as a pdb?* >>
I have load prmtop and restart file and then save PDB for coordinate(
*file.pdb).*

*>>When and how did you minimize the system?>>*
I have minimised the system. Giving the path for

*amber onprmtop file.prmtopcoordinate file.pdb*
I have used periodic cell boundary condition.

after minimisation system became unstable.

Regards

Aashish Bhatt

On Wed, Jun 6, 2018 at 7:42 PM, Brian Radak <brian.radak_at_gmail.com> wrote:

> 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
> system?
>
> 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 <aashish.ph16221_at_inst.ac.in>
> wrote:
>
>> 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 .rst.nc*(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 .rst.nc
>> file.
>> If i used VMD approach (mentioned above) then how can correct this
>> simulation.
>>
>>
>>
>> Regards
>> Aashish Bhatt
>> INST-Mohali
>>
>
>

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