VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Nov 05 2018 - 00:36:38 CST

Following your remarks, I checked all files again, discovering that no
parameters for ions had been made available.

Sorry for having not been careful enough before.

Thanks
fp

On Sun, Nov 4, 2018 at 2:47 PM Peter Freddolino <petefred_at_umich.edu> wrote:

> 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
>>
>