RE: Total charge problem

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Jul 04 2018 - 11:51:09 CDT

Hi Abhishek,

Did you ionize your system? By default, most ionization tools will add an extra 7 positive ions. An easy way to check the charge of just your protein would be something like:

puts [vecsum [[atomselect top "protein"] get charge]]

That ought to give you -7 as you expect.

-Josh

On 2018-07-04 06:56:17-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Deal all,
I'm setting up a simulation, during set-up my protein is showing 23 negatively charged and 16 positively charged residues. The problem is that while running the simulation system is showing
TOTAL CHARGE = 5.02914e-06 e .
According to calculation there should be total charge =-7, which is not the case here.
Can someone help me out in this problem.
***** Message from SEQRDR ***** THE SYSTEM CONTAINS 45 TITRATABLE GROUPS
 THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF
 HIS - 0 HSD - 0 HSE - 3 HSP - 0 ASP - 8 GLU - 15 LYS - 16 TYR - 3

Info: TOTAL CHARGE = 5.02914e-06 e
Thanks in advance,
Abhishek

This archive was generated by hypermail 2.1.6 : Thu Sep 19 2019 - 23:19:47 CDT