Gaff type for Mn2+ to run antechamber
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
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
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/addchar...
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
Same with add charge on chimera - Mn2+ is unidentified atomic type. On Wed, Sep 25, 2024, 3:27 PM Medhanjali Dasgupta < medhanjalidasgupta@gmail.com> wrote:
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/addchar...
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
Normally the electrostatic coloring is on the protein surface, and the Mn+ is not included inside the protein surface, so it's not involved in the calculation. I.e., the input PQR file would not include the Mn atom at all. It is useless to try to run Antechamber since you already know that the charge is +2, and Antechamber does not handle metal ions anyway. As it says in the help page link I sent before, "Note that Antechamber/GAFF are meant to handle most small organic molecules, but not metal complexes, inorganic compounds, or unstable species such as radicals, and may not work well on highly charged molecules. GAFF allows for parametrization of most organic molecules made of C, N, O, H, S, P, F, Cl, Br and I." Chimera's Add Charge tool works fine on strucures with Mn ions. For example, commands open 2mnr addh addcharge [... shows a dialog where you can click OK to designate MN net charge as +2 and SO4 net charge as -2, and then everything runs fine in a few seconds] Maybe you should ask the APBS help about whether you are really supposed to try to include the Mn in the PQR file and why +2 doesn't work.... we are not the APBS developers. In my personal opinion, you would not include the Mn anyway. Elaine
On Sep 25, 2024, at 1:28 PM, Medhanjali Dasgupta via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Same with add charge on chimera - Mn2+ is unidentified atomic type.
On Wed, Sep 25, 2024, 3:27 PM Medhanjali Dasgupta <medhanjalidasgupta@gmail.com> wrote: 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
Thank you, very helpful! On Wed, Sep 25, 2024, 3:42 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Normally the electrostatic coloring is on the protein surface, and the Mn+ is not included inside the protein surface, so it's not involved in the calculation. I.e., the input PQR file would not include the Mn atom at all.
It is useless to try to run Antechamber since you already know that the charge is +2, and Antechamber does not handle metal ions anyway. As it says in the help page link I sent before,
"Note that Antechamber/GAFF are meant to handle most small organic molecules, but not metal complexes, inorganic compounds, or unstable species such as radicals, and may not work well on highly charged molecules. GAFF allows for parametrization of most organic molecules made of C, N, O, H, S, P, F, Cl, Br and I."
Chimera's Add Charge tool works fine on strucures with Mn ions. For example, commands
open 2mnr addh addcharge [... shows a dialog where you can click OK to designate MN net charge as +2 and SO4 net charge as -2, and then everything runs fine in a few seconds]
Maybe you should ask the APBS help about whether you are really supposed to try to include the Mn in the PQR file and why +2 doesn't work.... we are not the APBS developers. In my personal opinion, you would not include the Mn anyway.
Elaine
On Sep 25, 2024, at 1:28 PM, Medhanjali Dasgupta via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Same with add charge on chimera - Mn2+ is unidentified atomic type.
On Wed, Sep 25, 2024, 3:27 PM Medhanjali Dasgupta < medhanjalidasgupta@gmail.com> wrote: 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/addchar...
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
participants (2)
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Elaine Meng -
Medhanjali Dasgupta