From: Christian Wohlschlager (Christian.Wohlschlager_at_jku.at)
Date: Thu Sep 15 2011 - 01:12:16 CDT

** Reply Requested When Convenient **

Hello !

I maybe fixed the problem of cionize : i did it the following:

I ve a pdp file which doesnt contain the charges of the protein so i
converted it to .psq with

 http://kryptonite.nbcr.net/pdb2pqr/ or another PDB2PQR Web Portal
read
:Generation PQR on this page

and then run cionize xxx.pqr (type help at the prompt)
after typing saveion yyy.pdb the i get the pdb file with coordinates of
the IONS.

Still i dont know how to get a NAMD MD with the two .pdb file
ORIGINAL.PDB abd IONS.pdb

thank you

christian
Christian Wohlschlager
JKU Universit├Ąt Linz
Altenbergerstr.69
4040 Linz
Austria