[gmx-users] calculation of pKa values

[Antonio Baptista]

On Mon, 22 Nov 2004, Peter Trodler wrote:

> Dear gmx users,
>
> there are several tools to calculate pKa values of residues of a protein 
> (TITRA,MCCE,MEAD,PDB2PQR,WHATIF). I am thinking which of this tools i should 
> use to protonate the residues by pKa value, because the results are 
> different, especially in the active site of proteins, and I don't want to 
> protonate by standard pKa values. It is not easy to compare the results with 
> experimental data, especially the protonation of ASP and GLU. Has somebody 
> already compared this tools and can recommend me which tool I should use ?
>
> I appreciate any help.

You can have a look at a previous gmx-users message:
http://www.gromacs.org/pipermail/gmx-users/2004-October/012846.html

> Best regards,
>
> Peter Trodler

Regards,
Antonio

--
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica, EAN, ITQB II, Apartado 127
2781-901 Oeiras, Portugal
phone: +351-214469619         email: baptista at itqb.unl.pt
fax:   +351-214411277         WWW:   http://www.itqb.unl.pt/simulation/
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