Re: Total charge problem

From: Abhishek Kumar Singh (bo13m1002_at_iith.ac.in)
Date: Thu Jul 05 2018 - 13:29:40 CDT

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>
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 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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