VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Nov 04 2018 - 03:08:49 CST

Hi
I got confusing error messages while running psfgen (vmd text mode)

> psfgen) building segment CAB
> psfgen) reading residues from pdb file parts/CA_segnCAB.pdb
> psfgen) unknown residue type CAL
> psfgen) extracted 1 residues from pdb file
> psfgen) disabling angle autogeneration
> psfgen) disabling dihedral autogeneration
> psfgen) Info: generating structure...psfgen) unknown residue type CAL
> failed!
>
> The same for MG reside type

Actually, both calcium and magnesiums are correctly defined in directory
/parts:
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 CAL CAL X 435 32.283 47.829 6.270 1.00 0.00 CAB
CA
END

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 MG MG X 434 14.606 47.830 14.074 1.00 0.00 MGB
MG
END

and along the .gen file:

segment CAB {
  pdb parts/CA_segnCAB.pdb
  auto none
}

segment MGB {
  pdb parts/MG_segnMGB.pdb
  auto none
}
while the .str streaming file reads
RESI CAL 2.00 ! Calcium Ion
GROUP
ATOM CAL CAL 2.00
PATCHING FIRST NONE LAST NONE

RESI MG 2.00 ! Magnesium Ion
GROUP
ATOM MG MG 2.00
PATCHING FIRST NONE LAST NONE

MASS 7 MG 24.30500 ! Magnesium Ion

MASS 9 CAL 40.08000 ! Calcium Ion

I left the matter standing a couple of days without resort. Therefore I am
here asking for advice. Calcium and magnesium are X-ray diffraction
identified ions belonging to either the protein or ligands. I am aware that
charmm parameterization of ++ ions is a developing matter..
Thanks
francesco pietra