VMD-L Mailing List

From: sarah k (dailycolors_at_gmail.com)
Date: Thu Dec 10 2009 - 00:07:06 CST

Dear Yu Fung,
i had the same problem. it's what i did and worked after guidance of John
and Peter:
after the QM calculations, save them into a pdb file. i call it qm.pdb. then
choose paratool. choose your initial pdb file as parent molecule and your
qm.pdb file as your base molecule. then do whatever you had done before:
1- choose atom types and assign VDW parameters (if some vdw parameters for
the atom types are missed, you'll face errors in the next steps)
2- autogenerate all the coordinations.
now you can save your topology and parameter files in the file menu.
if you've transferred your ligands from another software, get sure that all
your atoms have a unique name. otherwise change the name of each atom and
start the process (qm and paratool) by your new pdb file.so your ligands
won't break down in the next step like my molecules!
if you have just one single ligand you can go to autopsf generator and
remove the top_all27_prot_lipid.inp file and replace it with the topology
file you have written in the previous step. now you shouldn't have any
problem.
if you're using the ligand beside any other biological molecule, you should
(if you're using windows as i guess) add the components of your topology
file to top_all27_prot_lipid.inp in wordpad and save the file in *.txt
format. so this file should be used instead of the original *.inp file.
hope it works correct and accurate for you. i tried to mention all the
details to prevent errors.
Enjoy life,
Sarah