How do you add new small molecule topology to a forcefield?

24 September 2021 3 9K Report

I want to analyze the interaction of an enzyme with small molecule of an FMN (flavin mononucleotide) but gromacs doesn't recognize FMN. It require for manual definition of FMN topology.

Using SwissParam, i have generated .itp file for FMN, but failed to understand how to incorporate it into the forcefield file. I am using CHARMM36 ff.

I'll include the files of FMN generated by SwissParam

Ricardo J Ferreira

Hi,

you just have to add "FMN.itp" to "topol.top" as:

#include "FMN.itp"

But probably you will have to remove the [ atomtype ] and [ pairtypes ] and adjust some atoms to the CHARMM36 forcefield in GROMACS.

Aashish Bhatt

Kindly look

http://www.mdtutorials.com/gmx/complex/index.html

If your problem force field generation then try

Ligpargen server

Jonathan Purnomo

Thankyou Ricardo and Aashish, I was having problems in generating the FMN topol. I was following the instruction on gromacs tutorial but stuck on python error "python cgenff_charmm2gmx.py" and still trying to resolve it.

[Update]

i am now able to successfully add FMN topol, the steps are as in the gromacs tutorial

http://www.mdtutorials.com/gmx/complex.html

I listed the problems while performing ligand analysis, as well as the solution that works for me:

1. "perl sort_mol2_bonds.pl jz4.mol2 jz4_fix.mol2" command not working

Solution: i still have no clue why it happen, but when i use linux computer installed with the same version of python, it work.

2. Numpy was not recognized

Solution: instead of "sudo install numpy" try do "sudo install python3-numpy"

3. Decorator and NetworkX was not recognized

Solution: after sudo install decorator, if the problem still exist, try copying the decorator file into your working directory

4. cgenff_charmm2gmx version not compatible with Decorator and NetworkX

Solution: install the right version, i am right now using

"cgenff_charmm2gmx_py3_nx2" with "Decorator 3.4.0" and "NetworkX 2.3" and used the command

"python3 cgenff_charmm2gmx_py3_nx2" instead of

"python cgenff_charmm2gmx_py3_nx2"

note: cgenff_charmm2gmx_py3_nx2 can be downloaded from

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

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