From 590777c718951211d91712cac8b6575786a5eda8 Mon Sep 17 00:00:00 2001 From: Anne Kiirikki Date: Tue, 26 Oct 2021 17:03:58 +0300 Subject: [PATCH] Fixed AddData.py --- Scripts/BuildDatabank/AddData.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/Scripts/BuildDatabank/AddData.py b/Scripts/BuildDatabank/AddData.py index 50ac8eb99..3c2a82953 100644 --- a/Scripts/BuildDatabank/AddData.py +++ b/Scripts/BuildDatabank/AddData.py @@ -424,6 +424,17 @@ u = Universe(top, traj) u.atoms.write(dir_tmp+'/frame0.gro', frames=u.trajectory[[0]]) #write first frame into gro file +try: + u = Universe(top, traj) + u.atoms.write(dir_tmp+'/frame0.gro', frames=u.trajectory[[0]]) #write first frame into gro file +except: + conf = str(dir_tmp) + '/conf.gro' + print("Generating conf.gro because MDAnalysis cannot read tpr version") + os.system('echo System | gmx trjconv -s '+ top + ' -f '+ traj + ' -dump 0 -o ' + conf) + u = Universe(conf, traj) + u.atoms.write(dir_tmp+'/frame0.gro', frames=u.trajectory[[0]]) #write first frame into gro file + + gro = str(dir_tmp) + '/frame0.gro' u0 = Universe(gro) @@ -606,6 +617,10 @@ print("Date of adding to the databank: " + sim['DATEOFRUNNING']) +# Type of system is currently hard coded because only lipid bilayers are currently added. +# When we go for other systems, this will be given by user. +sim['TYPEOFSYSTEM'] = 'lipid bilayer' + # BATUHAN: add openmm parser # # # Save to databank