RE: Total charge problem

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Jul 05 2018 - 15:22:24 CDT

Hi Abhi,

Did you load a psf? Or some other file that tells VMD what atoms should have what charges? If you just load a pdb, that does not contain charge information, and then you'll also get 0, since it defaults to 0.

-Josh

On 2018-07-05 12:29:45-06:00 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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