RE: atom charges for protonated carboxyl termini

From: Peter Jones (
Date: Mon Feb 22 2010 - 18:46:25 CST

Dear Elia,

at there's a patch "PRES CTRP2" and accompanying parameters. I'm not sure why it has two protons, I have used the attached patch and parameters,


From: [] On Behalf Of Zumot, Elia Nabil []
Sent: Tuesday, February 23, 2010 7:48 AM
Subject: namd-l: atom charges for protonated carboxyl termini

Hi all,

Could anybody tell me the charge distribution on the atoms of an amino acid when the carboxyl group is protonated (provided the N-terminal is also protonated)?
I'm trying to create a psf file using the AutoPSF plugin and haven't been able to find a patch for a protonated carobxyl terminal of the protein. (An ASPP or GLUP patch would not be precise in this case since the CA is bonded to an amino group).

Is there an easier way that I am missing instead of reconstructing the topology file?

Thanks in advance

Elia Zomot

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