how to know the net charge of my system
Dear all, I'd like to know if there is a way to know the net charge of a system when opening the pdb file with Chimera. If so, is it possible to do it by means of the command line? Thanks in advance, Sara
Hi Sara, You could get an estimate by using Add Charge, which requires using AddH first. If you need commands they are simply addh addcharge ... and then look in the Reply Log (in menu under Favorites) for the net charge. However, Chimera does NOT do any detailed pKa predictions, and will assume that Asp, Glu are always negatively charged, and Lys, Arg always positively charged. His (histidine) may vary depending on its local H-bonding pattern. Also, if you have nonstandard residues like ligands, it may take longer (and sometimes fail) to calculate their charges. If you want a more careful estimate of the charge of a protein with pKa predictions, you may need to use some other program(s), e.g. PROPKA/PDB2PQR <https://server.poissonboltzmann.org/pdb2pqr> <https://www.ddl.unimi.it/vegaol/propka.htm> H++ <http://biophysics.cs.vt.edu/> However, I don't remember if these servers report the net charge in a simple way or whether you'd have to add up the charges yourself to figure out it. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 28, 2021, at 2:28 AM, Sara Luz Gomez Maya via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all, I'd like to know if there is a way to know the net charge of a system when opening the pdb file with Chimera. If so, is it possible to do it by means of the command line? Thanks in advance, Sara
Dear Elaine, Thank you very much for your prompt reply. It helped me a lot. Sara On Mon, Jun 28, 2021 at 8:16 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Sara, You could get an estimate by using Add Charge, which requires using AddH first. If you need commands they are simply
addh addcharge
... and then look in the Reply Log (in menu under Favorites) for the net charge.
However, Chimera does NOT do any detailed pKa predictions, and will assume that Asp, Glu are always negatively charged, and Lys, Arg always positively charged. His (histidine) may vary depending on its local H-bonding pattern. Also, if you have nonstandard residues like ligands, it may take longer (and sometimes fail) to calculate their charges.
If you want a more careful estimate of the charge of a protein with pKa predictions, you may need to use some other program(s), e.g.
PROPKA/PDB2PQR <https://server.poissonboltzmann.org/pdb2pqr> <https://www.ddl.unimi.it/vegaol/propka.htm>
H++ <http://biophysics.cs.vt.edu/>
However, I don't remember if these servers report the net charge in a simple way or whether you'd have to add up the charges yourself to figure out it.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 28, 2021, at 2:28 AM, Sara Luz Gomez Maya via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear all, I'd like to know if there is a way to know the net charge of a system when opening the pdb file with Chimera. If so, is it possible to do it by means of the command line? Thanks in advance, Sara
participants (2)
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Elaine Meng -
Sara Luz Gomez Maya