VMD-L Mailing List

From: Nilesh Ingle (nileshingle_at_gmail.com)
Date: Thu Oct 08 2009 - 21:47:14 CDT

Hello Everybody,
I am trying to model the absorbency of lysine residue on a SiO2 surface. I
have gotten to the point where I have a combined pdb and psf files of lysine
sitting on top of SiO2 monolayer.

In vmd when I pullup the window for namd, everything looks good. Except for
the parameter files !!! Right now I have two of these files. One for SiO2
generated while creating the monolayer (plugin Inorganic Builder). Second
file is default CHARMM parameter file for proteins.

My problem is when I add these two files using 'Add' in the parameter files,
the simulation does not run. It gives error moleid not found among others.

After going through both the parameter files, it seems there is no
"protein-si interactions" (such as C-Si-C or O-Si-O or C-Si-O).

So I was wondering if there is any 'parameter' file for "protein-siloxane
interactions" that can be input for running namd ?

Thank you for your time and kind attention. Your help is much appreciated.

Best Regards,
Nilesh.