how to distribute 20 polymers (ligand) randomly around the target protein to study interactions

User discussions
1

GROMACS version:2021.4
GROMACS modification: No
Hello everyone, I am new to GROMACS and trying to run protein-ligand simulations to consider protein-polymer interaction for the drug delivery study. So I want to randomly distribute 20 polymers around the target protein. How can I do it? Please kindly guide me in this regard. (I’m using gromos96 54a7 force field via gromacs 2021.4)

Thank you

2

Use gmx insert-molecules.

3

Thank you very much for your kind reply.
I am going to add 3 types of molecules (A, B and C) to my simulation box, so that first A and B molecules are added to the box, and after they interact with each other, C is added, and C interacts with the A&B mixture. For this purpose, I plan to do the following process in gmx insert-molecules .

My procedure: With each call of gmx insert-molecules I insert one type molecule, then use the output from that step as the input for the next to insert another type of molecule. Is it correct?

Thanks, regards

4

This is correct.

5

Thanks a lot…

6

I want to generate a topology file for a copolymer like PLGA with 1100 atoms to use in charmm forcefield. As you know, cgenff calculates topology files for molecules with less than 384 atoms. How can I solve my problem and which software should I use for my purpose?

7

You have to create RTP file in the required ff as well as take help from other software packages like Swiss param to fill the parameters in RTP file.Make sure don’t blinded accept parametrized values!