From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Fri Jul 06 2018 - 18:50:36 CDT
Have you done what Josh suggested? Is the charge on the protein -7?
On 05/07/2018 2:29 PM, Abhishek Kumar Singh wrote:
> Dear Josh,
> I did not ionize the system. I did use the above-mentioned code to
> calculate the total charge of different types of protein system and
> it's showing total charge zero for all systems. I don't understand,
> where is the problem?
> Thanks for your reply,
> On Wed, Jul 4, 2018 at 10:21 PM, Vermaas, Joshua
> <Joshua.Vermaas_at_nrel.gov <mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
> 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.
> On 2018-07-04 06:56:17-06:00 owner-namd-l_at_ks.uiuc.edu
> <mailto: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,
> Thanks & Regards,
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