[gmx-users] CMAP error

[Jon Mujika]

Dear Justin,

Thanks for your advice. You were wright. The problem was solved adding
the new residue name to residuetypes.dat

The issue was that when pdb2gmx found an unknown residue name, it
defined as "Others" system instead of "Protein". As a consequence,
the chain was capped there, adding a COO- termination to the "last"
residue of the protein.

Thanks again for the fast and efficient answer.

Jon

> I can't promise a solution, but you could try adding LSN and whatever other
> non-standard residues you need to use in residuetypes.dat.  I noticed that LSN
> is not there, which seems like an omission, since the other CHARMM-specific
> residue names are there.  When LYS is present, probably pdb2gmx is correctly
> interpreting the residue as protein before converting its name.  In the case of
> LSN or any other non-standard residue, this may not be the case.  Check the
> output of pdb2gmx carefully for any messages that might indicate that a residue
> of type "Other" was detected.  I've had this cause other problems.

> If adding LSN to residuetypes.dat fixes the problem, I will file a bugzilla.

> -Justin