VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Nov 04 2018 - 07:48:48 CST

It would be helpful if you could post your complete psfgen script, the
topology files that you used, and the full log/error output instead of the
excerpts. I wonder if the topology files weren't read correctly...
Best,
Peter

On Sun, Nov 4, 2018 at 5:16 AM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> 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
>