Hi.
I am trying to create ligand topology and parameter files using SwissParam webserver. I followed all the steps to create the .mol2 file available in SwissParam page: https://www.swissparam.ch/SwissParam_mol2_file.html.
But this error keeps on coming:
Unfortunately, topology and parameters were not successfully generated for LIG.mol2. A failure report can be found below. Failure report: Possible problem with molecular topology in LIG.mol2. SwissParam will try to reconstruct the topology from coordinates only. Topology and parameters were NOT generated. Please check the validity of your molecule. - Are all hydrogens present in the mol2 file? - Is the mol2 file correct? Please, read "How to obtain a correct mol2 file?" in the www.swissparam.ch website.
For reference, I am providing my ligand.mol2 file and lig_fix.mol2 which I have created for performing protein-ligand simulation using Gromacs and CHarmm27 forcefield.
Please help me solve this query.
Thank you for consideration.
Alvea Tasneem
Try ligpargen server using smiles format that might work for you.
All the best!!
If you could share which force field you are planing to use, then I can tell some alternatives. And I also look at the structure were I could see I hydrogen atom should be added to make it a stable structure. Let me know more about this.
Ajit Kumar Singh I am planning to use CHARMM27 force field. I have other complexes with different ligands which i have performed simulation using CHARMM27 that's why i have to use the same with this one as well for comparative analysis.
Alvea Tasneem In that case you can try Charmm-GUI (https://www.charmm-gui.org/) to generate. Its just that you will need a PBD structure (from RCSB database) where you have your ligand of interest. Or you will have to draw it manually.
Steps:
Charmm-GUI --- Input Generator --- Ligand Reader & Modeler --- Load PDB ID/ Draw the molecule
And you can try the topology generated here.
Ajit Kumar Singh Yes thank you so much for your guidance. I was able to successfully generate topology file for my ligand.
Since it takes the original smiles id of the ligand and generated pdb file with different coordinates than the one bound to the protein, I thought of creating smiles id of Lig_fix.mol2 file using DS visualizer.
Using that SMILES Id I input it into the CHARMM GUI and came to identify the mistake in the structure there was one extra double bond. I replace it with a single bond, and now it is giving me the correct topology in SwissParam as well as CHARMM GUI.
So thank you so much for helping me solve the problem.
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