From: Abhishek Kumar Singh (bo13m1002_at_iith.ac.in)
Date: Sat Jul 07 2018 - 11:42:15 CDT
Dear Victor,
I calculated the total charge as suggested by Josh but its not showing the
-7 charge (Calculated charge 5.029141902923584e-6).
I have done one more calculation with another system where charged residues
(as shown below in the mail) are ASP = 15 GLU = 21 LYS = 6
So, if we apply simple mathematics here it should be (-15-21+6) -30 but its
showing -26.
***** Message from SEQRDR ***** THE SYSTEM CONTAINS 61 TITRATABLE GROUPS
THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND
RTF
HIS - 0 HSD - 0 HSE - 11 HSP - 0 ASP - 15 GLU - 21 LYS - 6 TYR
- 8
Thanks
Abhi
* <nitwamitkumar_at_gmail.com>*
On Sat, Jul 7, 2018, 5:20 AM Victor Kwan <vkwan8_at_uwo.ca> wrote:
> 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>
> 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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