[gmx-users] Atom MNZ1 in residue LYS 107 was not found

[Steven Neumann]

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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