Maybe you could try the CCPBioSim mailing list in case someone there could help.
Best wishes James On 25 Sep 2024, at 19:19, Medhanjali Dasgupta <medhanjalidasgu...@gmail.com> 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 onkine server hosted at poissonboltzmann.org<http://poissonboltzmann.org/> to run pdb2pqr and apps but run into the problem of not knowing what the atomic charge is for Mn2+. Any ideas? Thanks in advance, Medhanjali ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
