Dear Gmx Users, I run implicit simulation for 1 us with virtual sites on hydrogens, then using VMD extracted coordinates into the pdb file. As I want to run explicit solvent simulation now I removed hydrogens so that pdb2gmx will add them. Then I got an error while trying to pdb2gmx using Charmm27:
Atom MNZ1 in residue LYS 107 was not found in rtp entry LYS with 22 atoms while sorting atoms. How come this atom appears in my pdb file? Any suggestions? Thank you, Steven
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