Dear APBS users.
I am trying to calculate an MMPBSA. I already have the snapshots taken from MD, and now I want to calculate the PB part using APBS. Currently I have been using APBS within Python Molecule Viewer ( MGL_Tools) and everything is working fine, but my problem goes as follow : My MMPBSA is oriented towards the calculation of the DG of binding between two proteins and at 2 differen pHs so I have in total 500 pdbs (snapshots) wich I don’t want to process with APBS/Python MV mannualy.
So How can I automatize this process? Should I define a Macro with VISION (from the same MGL / Python tools)? And if so could any one helpe in thath way? Or there is another way similar to the perl scripts to automate the process? Or should I use APBS as standalone and then automate it ?
Please, a lot of Help….
Center for Genomic And Bioinformatics