AMBER Archive (2009)
Subject: [AMBER] MM-PBSA and NetCDF
From: Bradshaw, Richard (richard.bradshaw08_at_imperial.ac.uk)
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?
-- Richard Bradshaw Mres/PhD Student, Chemical Biology Centre Room 537, Chemistry C1 Imperial College London South Kensington Campus SW7 2AZ