Hi, I use pdb2gmx command to convert a pdb file to a .gro and .top file(using CHARMM forcefield). For the C terminus, I use the CT3 option which is NCH3. When I use editconf to get a pdbfile from the .gro file generated, the C=0 and the NCH3 seem to clash in space in pymol.
Is there a way of correcting this? Pooja -- Quaerendo Invenietis-Seek and you shall discover.
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