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

Peter C. Lai pcl at uab.edu
Mon Apr 16 15:38:38 CEST 2012

Sounds like a bad VMD selection that didn't remove MNZ1 when you did the
conversion. MNZ1 sounds like a virtual site for the extra hydrogen off NZ
in protonated LYS.

On 2012-04-16 02:32:09PM +0100, Steven Neumann wrote:
> 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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Peter C. Lai			| University of Alabama-Birmingham
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