VMD-L Mailing List

From: Grazia Daminelli (Grazia.Daminelli-Widany_at_TU-Berlin.DE)
Date: Mon Feb 26 2007 - 02:35:27 CST

Hello

I want to generate the internal coordinates of my system, starting from
the pdb file and using paratool. I am loading my structure as "base
molecule" and then asking paratool to autogenerate the internal
coordinates. Bonds, angles, dihedrals are generated correctly, improper
bonds are missing, so after picking the appropriate atoms I generate
them with the "add coordinate" facility. In order to save the internal
coordinates table in a file, I use the command "write topology file".
But the values written in the topology file do not correspond to the IC
values I can read in the "internal coordinate" windows and the IC
improper are just missing. What happens during the writing of the
topology file? Which values are written there?

Thanks for your help

Grazia