[gmx-users] Re:How to define the protonated state of a protein

Antonio Baptista baptista at itqb.unl.pt
Fri Oct 29 13:43:37 CEST 2004

Hi, PeiQuan Chen,

In addition to methods based on dielectric-screening functions (as 
Mehler's program suggested by Xavier) you can use methods based on the 
Poisson-Boltzmann equation. A popular program of this kind is Don 
Bashford's MEAD, which you can get at http://www.scripps.edu/mb/bashford/. 
The program gives you a matrix of intrinsic and pairwise electrostatic 
terms, which you can then use to compute the actual protonation extents, 
eg, using a Monte Carlo method. If you are interested I can send you our 
own Monte Carlo program, MCRP (you can have a look at our lab page, given 

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/

On Fri, 29 Oct 2004, PeiQuan Chen wrote:

> Dear gmx-users£¬
>> The protonation state for a residue in a particular protein may be
>> different from the residue's protonation state in solution, so to be more
>> confident you have it right you need to do a pK calculation, which takes
>> into account other charges in the protein and the fact that the bulk of the
>> protein has different dielectric properties from electrolyte.
> Thank you for Eric respond. Does anybody have experience in pKa calculation?
> Do you mind telling me which software which is free to obtain to do these Job?
> Thank you in advance!
> Sincerely yours
> ----
> PeiQuan Chen
> ________________________________________________________________________
> PeiQuan Chen, Ph.D Student, Department of Chemistry, Nankai University
> WeiJin Road 94, TianJin, 300071, P.R.China
> phone:	(86)2223507510(HOME) (86)23505264 Mobile Phone: (+86)13920675030
> pqchen at mail.nankai.edu.cn
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