Starting at Xplor-NIH 2.26 (now it’s version 2.29 on Feb. 8th, 2012), official Xplor-NIH package provides an example script doing explicit solvent refinement. The short description made by Xplor-NIH author:
refinement with explicit solvent and full electrostatics. Includes rdcs, noes, jcoupling terms and dihedral restraints. This is a work-in-progress. Please compare with other protocols. In particular, this protocol seems to result in structures for which the DIHE term is large.
Note on J-coupling violations:
Calculated structures exhibit at least four consistently violated J-coupling restraints. These restraints are at or near mobile loop regions where the single structure approximation breaks down. In these regions an ensemble of structures must be used to fit all experimental data. Please see the gb3_ensemble directory for an example of ensemble refinement.
The script can be found (after version 2.26) at : XPLOR-NIH HOME/eginput/gb1_rdc
I did a quick try using a 90-aa protein–a small protein I am working on determining the solution structure. The input structure was originally refined by the refinement script provided by Xplor-NIH (with NOE, CDIH, RDC) from simulated annealed templates. The structural quality after regular refinement has been improved a lot ( by checking the Ramachandran plot: from ~60% to 85%). But the water refinement makes the solution structure better (85% –> 95%) although a lot of DIHE violations are noted by Xplor-NIH (same issue as issued by the author).
1. Ramachandran plot of structure refined by NOE, CDIH and RDC only.
2. Structure in #1 was refined by water refinement
3. Molprobity analysis of structures in 1 (up) and 2 (down) (click to see full sized snapshots)