[gmx-users] [Fwd: charge groups - short question]

[Anton Feenstra]

David wrote:
> -----Forwarded Message-----
> 
> From: Dr. Csaba Hetenyi <csabahete at yahoo.com>
> To: David <spoel at xray.bmc.uu.se>
> Subject: charge groups - short question
> Date: 02 Mar 2003 05:53:46 -0800
> 
> Hej David, 
> 
> I am performing GROMACS simulations for drug-protein
> systems and will make LIE at the end.
> The program works well, for 3500 atoms a 2ns dynamics
> takes 10 days on the PIV with that GHz...:)
> ---
> My ligand has some non-aminoacid parts. First, i just
> made it with the prodrug server, and let it give 0
> charge for some non-AA atoms. Now, i am thinking about
> using a standard charge system for the ligands (eg.
> Gasteiger) as my other ligands have larger non-AA
> parts and i need to precisely compare them (the dGs)
> later.
> However, Gasteiger (and also other charge calculator
> possibilities) does not know anything about charge
> groups. I am wondering, if the whole ligand could be
> used as one charge group, as there is no hope to make
> integer charges for only some groups of ligands. Or i
> can just define some atoms for a group even if the
> total charge is only close to an integer?

Charge groups do not *need* to be integer charge, it is more or less
just a convention to do it that way. They *should* preferably as
close to *zero* charge, wherever possible. But, this is mainly important
for cut-off related effects. I imagine this is no longer a requirement
if you would use PME in stead (which is only slightly slower nowadays).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
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