VMD-L Mailing List

From: sarah k (dailycolors_at_gmail.com)
Date: Fri May 14 2010 - 00:16:34 CDT

Hi Josh,

Thanks. I’ve kept the default values in all steps. i tried other numbers of
minimization steps. it could just run minimization. It’s very important to
me to have an environment as close as cell conditions in my simulation. But
I removed the water box to see if it works. It finally ran the MD
simulation, too.

The number of atoms was right after each try but in my final try when the MD
was done, the ligand was broken, completely. (I actually saved the last
frame and opened it by another software)

When I say it can open it, i mean that the psf file is added successfully.
When I load dcd file it counts all frames and the file is added to the list
but i can't see any protein in the VMD display window.

The origin structure is an organic compound docked into a protein and
immersed into water box. I’ve made the topology and parameter files, myself
by using paratool and generating parameters using analog parameters when
needed. The rest was the same as tutorial.

Thanks for your guide.

Enjoy life,

Sarah