AMBER Archive (2008)

Subject: Re: AMBER: PEO-PLA/PCE

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Jan 18 2008 - 14:42:06 CST

Quoting Z Insepov <insepov_at_gmail.com>:

> Did anybody simulate a water solution of PEO-PLA/PCA diblock copolymers by
> AMBER, OPLS or by any other technique?

You need to find the elementary constituants corresponding to your
polymer. Then, the construction of your polymer should be
straighforward by simply repeating these elementary constituants.
Nucleic acid, proteins and oligosaccharides are non-regular
bio-polymers. In your PEO-PLA diblock copolymer case, the polymer is
only constitued by two constituants (if I well understood your
problem). These should be quite simple to set up. We are preparing the
release of many building block strategies in R.E.DD.B.; They should be
available soon; currently fighting with them ;-) You might also look
at the work of Cieplak et al. J. Comput. Chem., 1995, 16, 1357-1377
for the starting point for such a problem. However, you will not find
the direct answer to your problem in this article; "only" appraoches
applyable to nucleic acid & protein polymer building.

If you are interested you can contact me in private: I can run
R.E.D.-IV for your problem; this should be straighforward - if I well
understood your problem ;-) You could even imagine to set up a huge
force field topology database (FFTPDB) for diblock and triblock
copolymers or more generally for any type of polymers (HYDROPHOBIC,
HYDROPHILIC, DIBLOCK, TRIBLOCK, AMPHIPHILIC, FUNCTIONALIZED)...

regards, Francois

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