Hi Peter, 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). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html#stat...
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. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge...
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). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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.
Thanks -pjb