The attached .tgz file contains CHARMM input and csh scripts for:

* importing PDB file 1IRK into CHARMM
* vacuum minimization with restraints based on B-factors
* constructing an RHDO of water
* combining the 1IRK model with the water, minimize
* ion addition by water replacement and energy evaluation
* heating from 210 K to 310 K with constant P
* NPT dynamics at 310 K

The archive contains a brief README.txt file; for additional explanatory material, see the Script Archive posts:

* complex PDB input examples
* make RHDO via spherical cut from a box
* ion addition by selective water replacement

The csh script examples assume a PBS batch environment, and a cover script named 'mpicharmm' that handles CHARMM setup, esp. for parallel runs with MPICH.

16410-bld1IRK.tgz (753 downloads)

Rick Venable
computational chemist