[Chimera-users] Chimera pH
meng at cgl.ucsf.edu
Mon Aug 3 17:01:57 PDT 2009
Chimera does not have any options to generate protonation states at
different pHs. It just aims for a state that is reasonable for
physiological pH (i.e. near 7).
However, it sounds like you already have the desired protonation
states in PQR format. Unfortunately Chimera doesn't read PQR format
(although we would like to have that capability in the future) -- the
last two columns, charge and radius, are wider than the occupancy and
bfactor columns of standard PDB format.
One possibility is to simply edit the PQR files to remove the last two
columns, then read these now-acceptable PDB files into Chimera. That
retains the hydrogens as output from PDB2PQR. I'm not sure what you
mean by models... do you also need point charges? A disadvantage of
column removal is that the PDB2PQR charges will be lost. However, you
could use Add Charge in Chimera (or the addcharge command) to assign
charges, and there are several AMBER options. Because the hydrogens
are already present, less common protonation states such as neutral
Lys, Asp, Glu will be recognized correctly and assigned the
appropriate charges. Whether this approach is sufficient depends on
whether you wanted to use the specific charge set from PDB2PQR as
opposed to an AMBER charge set.
If you did want the exact charges from PDB2PQR, you could reformat
those charges (next-to-last column in the original PQR file) into an
attribute assignment file and reassign them with Define Attribute (or
command defattr), after reading in the edited PDB files (PQR files
with last 2 columns removed).
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Aug 3, 2009, at 4:29 PM, Peter Baker wrote:
> I am trying to generate models of my protein at different pH. Any
> suggestions as to run how to accomplish this? I do have PBD2PQR
> files for the different pH but I am not sure how to apply them.
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