[gmx-users] pdb2gmx CA -> CA2+ or not?

[David Mathog]

When a CA HETATM record goes through pdb2gmx in the resulting .gro
file it is still called "CA", even though in ffG43a1.rtp the matching
residue is CA2+.  Furthermore,  in the itp file it says:

   type      res  atom
1  CA2+   1  CA   CA  ...     (FORM A)

whereas for something like CYS2 it says:

1  CH2    9  CYS2 CB ...

So my question is, what is the rule supposed to be for renaming
residues?  My modified program renames amino acid residues in the
res column exactly like the original pdb2gmx but for CA it comes
up with:

1  CA2+   1   CA2+  CA ...    (FORM B)

which is different from the original program.

Are the rules supposed to be different for ions or is this a case
where the end user was supposed to manually rename CA to CA2+?

The original program does issue a warning (twice actually, which is
odd since there's only one HETATM line, although there is also
a HET line right after FTNOTE), which is:

Warning: 'CA' not found in residue topology database, trying
to use 'CA2+'. 

And it does use it - sort of.

In other words, all else being equal would it be better
if pdb2gmx emitted the relevant line like FORM B or FORM A, above?

Thanks,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech