Questions and problems?

Non-aqueous solvent

How can AMBER be set up to run with a non-aqueous solvent?

The easiest approach is to use LEaP, which supports different solvent models. Read the section entitled "Solvent models" in the AMBER User's Manual; this is section 2.9 on page 28 in the Amber8 User's Manual.

What types (MeOH, DMSO, etc) of different solvent boxes are available that have been suitably parameterized and tested?

Examine the contents of directory $AMBERHOME/dat/leap/parm. In Amber8 one finds parameter files, prefixed with frcmod which abbreviates FoRCe MODification, for chcl3, meoh, nma, and urea.

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