[gmx-users] Protein at given pH

[Erik Marklund]

Hi,

I've used the H++ server myself at times. My experience is that it's rather sensitive to the very fine detail of the input structure in some cases. I've had situations where H++ suggest one protonation state, then a short md simulation takes the system to a slightly different conformation that seem more prevalent but that yields another protonation state if sent to H++ again. Use all biochemical knowledge that you can muster to check that the output makes sense. Focus on residues that you suspect might be important for the overall question you address.

That said, pKa calculations are inherently difficult and can probably not be done reliably without lots of simulations. As such H++ probably come close to what we can currently accomplish within reasonable time for (nearly) static structures.

Best,

Erik

7 nov 2012 kl. 10.19 skrev Steven Neumann:

> Dear Gmx Users,
> 
> I am trying to simulate protein-ligand interactions at specific pH=5.
> I processed my protein.pdb into the H++. As I see from th titration
> curve of the entire molecule it appears that at pH=5 the total charge
> should be equal to 2. When I process the obtained pdb from the server
> to pdb2gmx using -ignh I get the total charge of -3. Can anyone
> explain me this?
> 
> In terms of small molecules how can I get parameters at specific pH? I
> am using Charmm and parachem.org does not support pH changes. Can
> anyone advise?
> 
> thank you,
> 
> Steven
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html