VMD-L Mailing List

From: Nick Palmer (tuf90798_at_temple.edu)
Date: Thu Jun 14 2018 - 13:27:56 CDT

Hello everyone, I am making a topology file for the chromophore in the
mCherry protein and I I need to add hydrogens to the molecule in order to
get IC values in a table. I have tried using molefacture, however every
time I add the hydrogens to the molecule and write it to a pdb, several
carbon atoms end up missing from the file. I have also tried getting the IC
values from the xbgf file generated from the molefacture, but it doesn't
generate anything I can really use. Is there an easier way to do this that
I am not aware of? 

-- 
Nicholas J. Palmer