From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Jul 04 2018 - 11:51:09 CDT
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.
On 2018-07-04 06:56:17-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
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,
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