Generating topolgy for ligand containing Arsenic

User discussions
1

GROMACS version: 2022.5
GROMACS modification: No

Hi,

I am trying to simulate a protein bound to a ligand containing arsenic atom. I am not able to get through the pdb2gmx step. I tried generating ligand topology using CgenFF Server as well but it throws up an error saying : attype warning: element (As) not supported;
skipped molecule. I tried searching in Charmm36-jul2022.ff directory and could not find parameters for arsenic. I guess I have to parameterize the ligand from scratch. I am not sure how to move ahead. I am new to this field. I also understand that this topic could be little off from the Gromacs mailing list perspective but I am hopeful about finding a solution here. Could some one help me in moving ahead please? my ligand molecule looks something like this:

Screenshot 2024-07-30 at 2.51.01 PM
Screenshot 2024-07-30 at 2.51.01 PM922×878 163 KB

The atom in the center (purple) is Arsenic.

Thanks in advance

2

Hi,

I think my previous post did not get much attention. I will be really grateful for any insightful suggestion from the experts.

Thanks and Best regards

3

Hi,

Sorry for repeatedly asking this question. Can I get some step-by-step tutorial for generating parameters for the ligand mentioned in my initial post.

I will be highly grateful for your help and support.

best regards

4

There are some atomtypes that the CgenFF Server doesn’t support, so you would either need to provide those parameters yourself or try a different forcefield (see this post).