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

[Ruben Martinez Buey]

> Hi all,

what about GROMOS96 topologies with Gasteiger charges?
Do you think is ti possible as well?
Thanks a lot,
cheers,
Ruben

>
> >
> > 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 |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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--
___________________________________________

Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144  28006  MADRID
Tlf: +34-91-561 18 00 ext. 4380
___________________________________________


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