Justin Lemkul писал 07-11-2012 16:20:
On 11/7/12 7:10 AM, Steven Neumann wrote:
On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
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.
Thank you Justin. So do not understand why this server produce pdb
file which is redundant as you have to use -his -glu etc. flags
anyway. According to pK - this server predicts pK for each residue
and
when my pH < pKa it is protonated, otherwise it is deprotonated,
right? How about pH = pKa ?
If you're using the H++ server, it has no connection to Gromacs in
any way. Your command line uses -ignh, so any hope of guessing the
protonation state from the input is lost and thus you have to use
interactive selection to counteract that effect or otherwise hope
that
all the atomic nomenclature is right so that pdb2gmx doesn't complain
too much.
Actualy you can use data from h++ server with GROMACS. In order to do
so you
need
1. amber files from H++ specificaly *.top and *.crd file
2. Install ambertools
3. Use ambpdb to create pdb file from *.top and *.crd something like
ambpdb -p
*.top < *.crd > *.pdb
4. Get my script to renumber pdb and inset chain ids from
http://biod.pnpi.spb.ru/~alexxy/h++/pdbfix.pl
5. Process amber pdb file with it.
6. Feed it to gromacs and chose amber frocefield. Now it will use right
protonation states
If pH = pKa, then your life is tougher. In solution, 50% of the
residues in the protein molecules will be protonated, 50%
deprotonated. You may have to model both protonation states if this
is the case.
-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
========================================
--
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Gatchina, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexx...@gmail.com
mailto:ale...@gentoo.org
mailto:ale...@omrb.pnpi.spb.ru
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