[gmx-users] Re: defining new residues?

Michael Brunsteiner mbx0009 at yahoo.com
Sat Nov 4 23:03:05 CET 2006

scott.t.milner at exxonmobil.com wrote: 

> It would be very
> convenient if I could add these structures as new "residues" to the
> definitions of some of the force fields (e.g., OPLSAA and GMX), so that I
> could use pdb2gmx to generate topology files for a simulation, without
> having to generate the topology files by hand. 

thats exactly what i did a few years ago in the course of
some research about using polymers as pigment dispersants,
I made some rtp entries extending OPLS-AA to include
residues (monomers) for common organic polymers such as 
polystyrene, poly acrylic acid and a few more. As charges
I used ESPD charges from HF calculations in Gamess.
Simulations including polymer chains of various chain
lengths and composition then became quite easy to set up.
Whether the OPLS VdW and non-nondond parameters are 
transferable to this kind of materials is a different
question, and that research project was terminated before
I could work out a definite answer there.
If you are interested in more details contact me 
off list ( micb at uic edu)

Everyone is raving about the all-new Yahoo! Mail 

More information about the gromacs.org_gmx-users mailing list