How to generate topology files (topol.top) lipid and user defined molecule mixture MD simulation?

User discussions
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1

GROMACS version: 2022

Dear all GRAMACS users,

I want to simulate a random mixture of POPC lipids and a new molecule (lipid anchor). CHARMM-GUI was used to generate the topology file (.itp) file for the lipid anchor. It also contains another .itp file (charmm36.itp) that has new bonded and none bonded parameters for the new molecule.

When I run grompp command following error was generated. May anyone help me to resolve the problem ?

Screenshot from 2022-09-17 03-31-45
Screenshot from 2022-09-17 03-31-45864×447 49.2 KB

2

The error means you’re somehow trying to incorporate multiple topologies that both include the highest-level directive for a force field. This isn’t allowed. The only real problem with using CHARMM-GUI inputs is that they are not designed to be modified, only used directly “out of the box” and any attempt to change the system usually leads to failures due to topology directives clashing, missing parameters, etc.

3

Thank you @jalemkul, Can you propose to me any method to resolve this problem ? (may be other tool to generate topology files )

4

The topology for a single entity should not #include a parent force field when used in conjunction with other species. Presumably what you actually have is a standalone .top for the lipid anchor that needs to have the #include "charmm36.itp" statement removed, but without seeing the files you’re using, that’s just a guess.

5

@jalemkul , I tried removing the “charmm36.itp” file from the topol.top file. Still, I received the following errors.
(see attachment)
I also attached the other charmm36.itp and top file with this for your reference. Please suggest me to resolve this problem

Screenshot from 2022-10-05 00-33-40
Screenshot from 2022-10-05 00-33-40892×964 85 KB

topol.top (812 Bytes)
charmm36 _itp.dat (56.9 KB)

6

Again, this is the pain of trying to modify something from CHARMM-GUi. It assumes you are building everything you need and it supplies only the relevant subset of the force field that applies to your system. In your case, it is giving you all the relevant CGenFF parameters for your species, most (if not all) of which are already present in the parent CHARMM force field (which contains everything, as is GROMACS convention).

Basically, your options are:

  1. Build the entire system with CHARMM-GUI
  2. Solve each of these errors individually (remove the parameters from the molecule’s .itp file so you use what is in the parent force field) so that you do not have conflicts.