[gmx-users] CMAP error

[Jon Mujika]

Dear all,

I am setting up a system with GROMACS 4.5.3 and the CHARMM force
field. In the protein, I have a neutral lysine, for which CHARMM force
filed has a specific residue type (LSN). When I wrote LSN as residue
name in the initial pdb file, the topology file was perfectly created
by pdb2gmx. However, in the next step, grompp complained about the
CMAP torsion between the two previous residues:

Fatal error:
Unknown cmap torsion between atoms 2747 2749 2751 2754 2757

However, if the LYS residue was written in the initial pdb file and
the -lys option included with pdb2gmx (chosen the neutral protonation
state for this lysine), grompp did not complain.

The problem is that there is a deprotonated tyrosine (bound to a
metal) in my system. I created a new residue type, but again the
grompp complained about the CMAP between the two previous residues.
Unfortunately, in this case I can't fit the problem with any of the
pdb2gms options.
I think the problem arises when a non-standard residue is included in
the initial pdb file. Does someone else find this problem? I would
appreciate any advise about how to solve it.

Thanks in advance

Jon