Does the python script, i.e. cgenff_charmm2gmx_py3_nx2.py (for CHARMM36) also works for a different force field such as CHARMM27 or AMBER99 SB or GROMOS96 54A7 ?
if not, where can I find the script for (each respective force field) generating ligand topology files such as .prm, .pdb and .itp ?
Is there any other way you may suggest to generate ligand topology files such as .prm, .pdb and .itp ?
Thanks in Advance
Sachin Rajpoot try ligpargen/swissparam sever for ligand parameterization. For automated workfolw of P-L simulation can be conducted using Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...
No, they only work for CHARMM forcefields;
The best way is to use CHARMM-GUI to obtain the .prm and .str files that can then be used with cgenff_charmm2gmx_py3_nx2.py;
If you cannot use it, you can always try MATCH.
Thanks for answering @Ricaro @Harvinder
please help, I ran the following command for ligand parameterization:
python cgenff_charmm2gmx_py3_nx2.py lig lignew.mol2 ligand.str charmm36.ff
I am getting the following error:
Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (71) and top (0) are unequal
Usually this means the specified residue name does not match between str and mol2 files
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