Bad idea. Adding just one proton (1/Navogadro moles ~ 1.6 * 10^-24)to a
box of say 500 nm^3 (5 10^-22 liter), continaining roughly 10000 waters
would give a pH of 2.5 (-log[1.6/5*10^-2), which is the maximum pH you
can reach for such standard box. If you want to go higher, say to pH=7,
your box needs to be at least 1.6 * 10^-17 liter, or 1.6 * 10^7 nm^3.
THis is too big for simulation.
Therefore adding H+ or H3O+ is not really an option. Instead you should
choose the protonation states of the titrating sites in the system such
that they correspond to the pH your are interested in. Equilibrium
exchange of protons between aminoacid sidechains is probably happening
on a timescale much longer than a typical simulation length.
Gerrit
On Aug 8, 2006, at 9:16 PM, Arthur Roberts wrote:
Hi, Luisa,
I would first calculate the number of protons (H+)
that you would find your water box. Then I would use
the command genion to generate that number of H+'s
that corresponds to the pH. Then I would use grompp
to find out what the final charge is. If it is still
negative, I would add NA+. If it is positive, I would
add CL-. This should approximate the pH. Although
there is one problem, ionizable residues. You will
need to set those manually. I am not sure, if you can
use the morse potential on specific residues instead
of harmonic potential to make a residue ionizable. I
hope this helps.
Best wishes,
Art Roberts
University of Washington
Department of Medicinal Chemistry
--- luisa pugliese
<[EMAIL PROTECTED]> wrote:
Hello to everybody,
I am new to this mailing list and I am writing
because I wonder if anybody knows how can I set up
the pH of the system in gramacs.
Thank you to everybody
Luisa
=============================
Luisa Pugliese, Ph.D.
[EMAIL PROTECTED]
S.A.F.AN. BIOINFORMATICS
Corso Tazzoli 215/13 -10137 Torino - ITALY
tel +39 011 3026230
fax +39 011 3165080
cell. +39 333 6130644
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the
list. Use the
www interface or send it to
[EMAIL PROTECTED]
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Note, from 2005 on my email adress has changed to [EMAIL PROTECTED]
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
