On 11/7/12 4:19 AM, Steven Neumann wrote:
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?
pdb2gmx chooses protonation states based on the assumption that you're working
at neutral pH. If you want some alternate protonation state for certain
residues, you have to choose them yourself using the various options that
pdb2gmx provides for this purpose.
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?
pKa values for most common groups should make the protonation state at a given
pH fairly straightforward, otherwise you need to calculate the pKa's in some way
and adjust the molecule's protonation accordingly.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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