Build the Topology (adding .prm and .itp)

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1

GROMACS version: 2021.2
GROMACS modification: Yes/No
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Hello.
I am trying to calculate Molecular Dynamics for protein-ligand using GROMACS/CHARMM force-field.
I have a question…!
I’m trying to add a parameter file for the ligand to the topol.top file (like #include ~).
In this case, should I use both .itp and .prm? or Is it okay if I just use .itp? (Can I exclude .prm?)

The reason I am asking this question is because the following situation has occurred …

  1. Create .itp and .prm files using acpype
  2. and I added each fileto topol.top
  3. but an error occurred when I entered the command line (gmx grompp -f ions.mdp -c solv.gro –p topol.top -o ions.tpr)
  4. The error message is as follows; .prm & too few parameters on line
    Or Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

This may be a stupid question to some, but I would appreciate it if you could let me know…!
Thanks.

2

Kyle,
Why you using acpype for charmm? use charmm-gui.

3

This is because I am cautious about uploading the structure to the web and want to proceed locally.
Is there a way to create parameters locally other than acpype?

4

You could try GROMACS / STaGE · GitLab, but it requires open babel and MATCH (to generate CGenFF/CHARMM compatible topologies) and/or ACPYPE and antechamber (for GAFF/Amber compatible topologies).