RE: atom charges for protonated carboxyl termini

From: Peter Jones (Peter.Jones-2_at_uts.edu.au)
Date: Mon Feb 22 2010 - 18:46:25 CST

Dear Elia,

at http://www.charmm.org/documentation/c34b1/phmd.html 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,

cheers,
PJ

________________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of Zumot, Elia Nabil [enz1_at_pitt.edu]
Sent: Tuesday, February 23, 2010 7:48 AM
To: namd-l_at_ks.uiuc.edu
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

UTS CRICOS Provider Code: 00099F
DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not
read, use, disseminate, distribute or copy this message or attachments. If
you have received this message in error, please notify the sender immediately
and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority,
states them to be the views of the University of Technology Sydney. Before
opening any attachments, please check them for viruses and defects.

Think. Green. Do.

Please consider the environment before printing this email.


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:49 CST