[gmx-users] Topology utilities ?

Marc Baaden baaden at smplinux.de
Wed Mar 13 15:33:47 CET 2002

dava at davapc1.bioch.dundee.ac.uk said:
>> Well actually the non-server version of PRODRG can do that
>> (interactively delete/remove hydrogens (POLAR ones, that is)) before
>> writing out the final topology. Similar for changing chirality.
Is this version publicly available ? (or will it be ?)

>> Would it be useful to have that on the server as well? 
I would definitely say yes.
Eg as soon as you have a ligand binding to cations you might need it.
Also if you want to model organic anions (picrate, ..)
I have several structures for which it would be useful.


 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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