Dear All, I would like to ask for your help to my problem dealing with making topology file for ligand with OPLS-AA forcefield by following TutorialAcpypi4GromacsOPLS.
Now, let me show you my steps: - Getting my ligand.pdb file from PDB - Adding all hydrogen by PRODRG2.5 Server with GROMOS 87 forcefield, full charges, no EM, full chirality - Using antechamber to convert ligand.pdb to ligand_bcc.pdb (antechamber -i ligand.pdb -fi pdb -o ligand_bcc.pdb -fo pdb -c bcc) - Running ACPYPI (acpypi -i ligand_bcc.pdb), then obtaining folder ligand_bcc.acpypi, including my wanted file: ligand_bcc_GMX_OPLS.itp. However, some problems occured: 17 opls_x 1 MOL O24 17 -0.447600 0.00000 ; qtot -0.186 x 22 opls_x 1 MOL C4 22 -0.147400 0.00000 ; qtot -0.168 x It seems that OPLS-AA forcefield does not recognize what Amber forcefield have assigned for this atomtype/bondtype. Then, it stopped me there from running the next steps in order to perform modeling dynamics simulation of protein-ligand complex in Gromacs with OPLS-AA forcefield. Could you please help me to solve this problem? I really hope to hear from you soon! Thanks in advances!
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