Generating coordinates for ligand containing Cadmium using Charmm forcefield in Gromacs

User discussions
1

GROMACS version: 2022.5
GROMACS modification: No

Hi Dear Community Members,

I am new to this field and had a question. I am trying to simulate the interaction of a protein with couple of ligands that have cadmium and arsenic bound with coordination bonds. Is there a way I can generate the topology of these ligands using Charmm36 forcefield?

I am new to this and new some help.

Thanks in advance

2

Hi,

My previous post could not gather any responses. I will be really grateful if I can find some help in this thread. Basically my ligand is just two glutathione molecules joined together with a cadmium atom. I am attaching the ligand structure below:

GetImage
GetImage964×640 49 KB

How can I get the pdb2gmx to make the topology for this ligand. I tried a few times but could not succeed. I also tried to get the ligand topology files from CGENFF server but found out that apparently CGENFF also does not support cadmium. Upon closer examination, I also found that Charmm36 forcefield has parameters for Cadmium in the ions.itp file:

[ moleculetype ]
;Cadmium (II) cation
; molname nrexcl
CD2 3

How do I proceed from here? Any help or inputs will be highly appreciated.

Thanks and regards