Dear friends, i had a problem while running the of protein-ligand complex simulation, in which i have generated the ligand toplogy by using online Prodrg server and iam using gromos 96.1froce field.
there was an note and an error during minimization NOTE 2 [file trp.top]: The largest charge group contains 15 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Analysing residue names: There are: 223 Protein residues There are: 1 Other residues There are: 25853 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 161838.00 Largest charge group radii for Van der Waals: 0.790, 0.356 nm Largest charge group radii for Coulomb: 0.790, 0.399 nm WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (1.188798) is larger than rlist (1.000000) i am using the mdp file the one that i copied from gromacs protein-ligand tutorial can any one please explain these errors so that i can go farward in my work. and i have a doubt, as there are other updated forcefields, how much reliable is the gromos 96 ff.... -- Arun Kumar Somavarapu Project-JRF Dr. Prasanna's lab TMC, ACTREC Navi Mumbai-410210
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