AMBER Archive (2009)

Subject: [AMBER] MM-PBSA and NetCDF

From: Bradshaw, Richard (
Date: Wed May 27 2009 - 10:38:13 CDT

Dear all,

I have a couple of quick questions. Does anyone know if the MM-PBSA scripts (specifically make_crd_hg.f) have support for reading netcdf trajectories made by PMEMD (ioutfm=1 option), or would I have to convert back to amber format before analysis?

Also, if I were to combine the coordinates and velocities file into one (ioutfm=1 and ntwv=-1) would ptraj have any trouble in reading this, and/or would it be able to split the netcdf file into two amber formatted .mdcrd and .mdvel files?

Many thanks,


Richard Bradshaw
Mres/PhD Student, Chemical Biology Centre
Room 537, Chemistry C1
Imperial College London
South Kensington Campus

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