Hi all, I have done complex (protein + ligand) complex from autodock software using this complex im trying to follow
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html tutorial But when i take complex structure directly from autodock result and run PDB2GMX it will give error because it is not recognizing ligand topology which is in complex structure. Then i followed justin tutorial took protein alone and applied Charmm27 Force field and used generate ligand topologies using Swissparam tool ( http://swissparam.ch/) when i do Editconf and created cubic box ligand is going away from protein. Actually my main task to place ligand in paraticular binding site in my protein and perform molecular dynamics. Can any body tell me how to do this..? Thanks in advance -- Sainitin D
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