AMBER NetCDF file for Simulation

From: Aashish Bhatt (aashish.ph16221_at_inst.ac.in)
Date: Wed Jun 06 2018 - 07:33:10 CDT

• Next message: Brian Radak: "Re: AMBER NetCDF file for Simulation"
• Previous message: Francesco Pietra: "Sudden drop of /\A in ParseFEP.log near lamda 1.0"
• Next in thread: Brian Radak: "Re: AMBER NetCDF file for Simulation"
• Reply: Brian Radak: "Re: AMBER NetCDF file for Simulation"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

• Next message: Brian Radak: "Re: AMBER NetCDF file for Simulation"
• Previous message: Francesco Pietra: "Sudden drop of /\A in ParseFEP.log near lamda 1.0"
• Next in thread: Brian Radak: "Re: AMBER NetCDF file for Simulation"
• Reply: Brian Radak: "Re: AMBER NetCDF file for Simulation"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:09 CST