Hi Elaine,

When I try to generate the electrostatic surface with PDB2PQR and ABPS it requires an input.pqr file which is essentially just a pdb file but instead of the occupancies and Bfactors it contains all the atomic charges (electrons) and atomic radius (angstroms).

I am not able to figure out what this atomic charge (electrons) is for Mn2+. 2+ is an invalid input there.

So I found out you can run antechamber to figure out this value but when I go and run antechamber via chimera it cannot compute charges for Mn2+ as is it treated a sun identified atomic type.

Medhanjali

On Wed, Sep 25, 2024, 3:23 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

Dear Medhanjali,
Maybe I'm missing something, but the charge for Mn2+ is +2.  It's just a monatomic ion (a single atom) so there is only one atomic center and it gets all of the charge.

In Chimera, these are simply assigned their formal charges, and Antechamber is not used for them.  See the bullet points near the top of the Add Charge help page:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 25, 2024, at 1:13 PM, Medhanjali Dasgupta via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Dear all,
>
> I am trying to generate the electrostatic surface for a protein that contains Mn in the 2+ state in its active site.
>
> I've tried to go about it in two ways but keep getting stuck.
>
> 1. If I use chimera or Pymol to use the PDB2PQR-APBS plug in, it cannot find GAFF type for Mn2+ so it cannot run anyechamber to allocate the atomic charge to Mn2+.
>
> Am i missing an update? Is there any way to get around this? Can I run antechamber myself to recognise my ion of interest, and then determine the charge, input it into the .pqr file and run APBS?
>
>
> 2. I have used the online server hosted at poissonboltzmann.org to run pdb2pqr and apps but run into the problem of not knowing what the atomic charge is for Mn2+.
>
> Any help would be appreciated.
> Thanks!!!
> Medhanjali