Modeling Documents

Pick one frame from namd dcd file and save it to another single-frame dcd file

         This tool is helpful when one frame is needed but the entire trajectory is too large to transfer.

Convert NAMD binary restart file to amber restart ASCII restart file


Installing and compiling Amber12 with CUDA

        Description of how to install and compile cuda toolkit and Amber12 for the GPU machine (ubuntu OS).
        by Christopher C. Roberts and modified by Zhiye Tang
        TXT file

Organic Ligand Parameterization and Complexation with AMBER and AmberTools

Description of how to parameterize a custom organic ligand. Additionally describes how to form both a covalent and non-covalent complex with the newly parametrized ligand.
Written by Christopher C. Roberts

How to Run NAMD2 in Parrot of Biocluster using Charmrun

 /opt/NAMD-2.7_Linux-x86_64-parrot/charmrun ++local ++p <procs> /opt/NAMD-2.7_Linux-x86_64-parrot/namd2 <configfile>