https://github.com/kimjc95/addNewResidue.py
This code adds custom-made amino acids to the GROMACS forcefield directory.
Currently supporting AMBER and CHARMM forcefields.
This code was written by Joo-Chan Kim at Molecular Synthetic Biology Laboratory in Korea Advanced Institute of Science and Technology (http://msbl.kaist.ac.kr).
If you have any questions or improvements to make, please contact me through kimjoochan@kaist.ac.kr .
When you supply the .mol2 file of your amino acid with N-acetyl cap and C-methylamine cap, this code will
WARNING: This code only works for non-terminal residues!
Also, it simply add/subtracts charge change resulting from removing ACE/NME caps.
So the resulting atomic partial charges may not be accurate!
For the accurate parameterization, use other methods such as quantum mechanical ones.
Guide :
Name the heavy atoms (non-hydrogens) in your custom-made residue.
The atom names should be unique in the residue and must be less than 4 letters long!
You do not have to add hydrogen atoms.
Then save your .pdb structure with custom residue (without hydrogens).
For simplicity, remove all residues other than i-1, i, i+1 th ones from the .pdb file you made in step 1.
Change (i-1)th residue into acetyl group.
Change (i+1)th residue into N-methylamine group.
You may now add hydrogens according to the pH. You don’t have to name them, since addNewResidue.py will rename them afterwards.
(Make sure to check your hydrogens to have appropriate residue index! ((i-1) for ACE hydrogens, i for your residue, (i+1) for NME hydrogens))
Then save as the .mol2 file.
You may use external programs such as Chem3D or Avogadro.
or you may use the optimize plugin from PyMOL
Save the energy minimized structure as .mol2 file.
checkout acpype github.
To run the acpype, you have to unify residue names (change ACE and NME’s name into your residue’s) in your input .mol2 file.
But do not unify the residue indices! addNewResidue.py differentiates the ACE & NME caps from your residue by the residue index info in your .mol2 file!
checkout CHARMM-GUI website.
Sometimes CHARMM-GUI may not properly print out the improper dihedral infos for phenyl rings in your residue, so be aware of that!
Place the resulting folder in your working directory.
checkout GROMACS forcefields
Please note that there is an error in amber14sb_OL15.ff_corrected-Na-cation-params.tar.gz file made by mabraham, 08:29, 30 Aug 2019.
you should manually change line in ffbonded.itp file’s improper [ dihedraltypes ] section
CT CV CC NA 4 180.00 4.60240 2
into
CT CC CV NA 4 180.00 4.60240 2
to avoid errors you will face when running the simulation of systems containing HID residues.
for AMBER forcefield:
python addNewResidue.py -m NEW.mol2 -f amber14.ff -n NAME -a NEW.acpype
for CHARMM forcefield:
python addNewResidue.py -m NEW.mol2 -f charmm36.ff -n NAME -c charmm-gui-result
For the detailed info about the input format, use -h or –help flag.
If all is well, the aminoacids.rtp, aminoacids.hdb and atomtypes.atp files will not require further changes.
Check the newly created newffbonded.itp and newffnonbonded.itp files.
In case where there is no new bond / nonbonded interaction parameters to add, the newffbonded.itp and newffnonbonded.itp files will not be created.
If everything seems fine, change their names into ffbonded.itp and ffnonbonded.itp.
Enjoy simulation!