[apbs-users] Protonation status from PDB2PQR

[Weihua Geng]

Dear APBS team and users,

We are trying to calculate pKa value for solvated proteins and we use PDB2PQR to obtain charge distribution for a given protein at different protonation status. Following PDB2PQR manual, we know that the titratable residue has different titrating status using different name. For example, from unprotonated to protonated status,
ASP: ASP —> ASH
GLU: GLU —> GLH
TYR: TYM —> TYR
HIS: HIE —> HIP
LYS: LYN —> LYS

However, we met problems for CYS and ARG as described below.

CYS: It has two Names as CYX and CYM, but the PDB2PQR gives same result for these two names

ARG: There is no Amino Acid Residue Additions for ARG.

I wonder if there are any way to output the unprotonated and protonated status for CYS and ARG. Any hints will be highly appreciated.

Sincerely,

Weihua

-----------------------------------------------
Dr. Weihua Geng
Assistant Professor of Mathematics
Southern Methodist University
(214) 768-2252
http://faculty.smu.edu/wgeng
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[Nathan Baker]

Hi Weihua --

Juan is probably the best person to answer this question.  I've Cc'ed him on this email.

Thanks,

Nathan

[Brandi-Lozano, Juan M]

Hello Weihua, I’ll look into this and get back to you as soon as possible. Thanks!!

 

--Juan Brandi