Re- CHARMM(m) Solvation
Subject: Time:9:20 AM
OFFICE MEMO Re: CHARMM(m) Solvation Date:2/2/95
On 2 Feb., McCarron from the UK wrote:
"Could anybody out there tell me if it is possible to solvate
using CHARMM. I know that CHARMM can recognise molecules already
solvated but is it possible to solvate with this program like
you can with AMBER say.
Thanks for you help"
Yes, indeed ....... CHARMM, the program is quite well
suited for calculations on virtually all molecular systems.
Although its original design was to take advantage of biomolecular
systems, CHARMM has been used for materials, polymers, drug-design
and many many other non-protein/nucleic-acid type systems.
The CHARMM-Harvard and CHARMm-MSI force fields also, have
been parameterized to be compatible with several well-validated
water models, most notably the TIP3 model of Prof. Jorgensen.
Solvation of molecules, most easily accomplished through the
Quanta interface, can take the form of:
periodic boundary systems,
stochastic boundary systems
and pressure-gradient calculations.
In all these cases, it is trivial to solvate small molecular
systems with a 15A or a 30A box of TIP3 waters (provided),
or to solvate a subset of a much larger system with a
sphere of water.
We have recently been working up hexagonal cylinders
of water to use with coiled peptide, and nucleic acid
Mgr. Life Science Applications, MSI