7/11/2023 0 Comments What is chimera tool![]() Van der Waals parameters will be taken from the closest atom type in CHARMM22.įor consistency with CHARMM, atoms with identical names will be renamed. ![]() Only the harmonic part of the bond, angle and improper terms are retained If you upload a Mol2 file, the Merck Molecular Force Field (MMFF) will be used to derive CHARMM parameters for your ligand, as follows: carboxylate groups are usually deprotonated at physiological pH), and make sure that it has a correct topology (we recommand UCSF Chimera, OpenBabel, MarvinSketch, XDrawChem, ChemDraw).Īs a ZIP file containing files in the CHARMM format (PDB/RTF/PAR). Check atom chirality,Īnd adjust protonation states according to your needs (e.g. ![]() The structure of the ligand can be uploaded either:Īs a MOL2 file with all hydrogens and 3D coordinates. A success rate >80% can be achieved with drug-like ligand with less than 15 free dihedral angles.
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