Re: Total charge problem

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Fri Jul 06 2018 - 18:50:36 CDT

Hi Abhishek,

Have you done what Josh suggested? Is the charge on the protein -7?

-Victor

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,
>
> Abhi
>
> 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.
>
> -Josh
>
> 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,
> Abhishek
>
>
>
>
> --
> Thanks & Regards,
> Abhishek

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