Hi, I have a pdb file which contains a Cl ion. I have changed the corresponding line as follow:
HETATM 2629 CL-1 CL1 a 403 22.963 23.915 -56.184 1.00 16.70 Cl
but it does not work and the error message says: “Your PDB contains an elemental ion CL with inconsistent charge”.
I have also try to put
HETATM 2629 CL-1 CL-1 a 403 22.963 23.915 -56.184 1.00 16.70 Cl
but then this message pop-up: “ATOM/HETATM line does not meet the expected format”, I guess because I mess up the column format.
How should I do?
Thanks.
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Hi Beatrice
When defining a four character atom name in the PDB file, you have to shift it by one column to the left (without messing up of course the alignment of the other columns).
Probably the cause of the problem.
The atom name should be CL-1 and the residue name CL1
Thanks! I followed your indications, but it still did not work. The error message says "Your PDB contains an elemental ion CL with inconsistent charge”.
The columns look aligned. In the following example, the row of Fe2+ does not give any error.
The error is referred to the second row.
HETATM 2628 FE+2 FE2 a 402 29.110 19.097 -13.982 1.00 0.00 Fe
HETATM 2629 CL-1 CL1 a 403 22.963 23.915 -56.184 1.00 16.70 Cl
Any other suggestions? Thank you very much.
Please share the problematic file so that we can test on our side.
@Beatrice, thanks for reporting this error!
There was a small bug when getting the charges of negative ions, it has been identified and fixed, please try again! 