On Thu, Dec 06, 2018, Thomas Evangelidis wrote:
>
>Thank you for the explanation. It seems that at some point the TER records
>were deleted while I was removing the ligand from the complex. But still
>the last protein residue is 385 and all following atoms belong to waters
>with resid starting from 501. tleap should be capable of recognizing the
>C-term. After all, it does recognize it when it writes the intermediate pdb
>file (protein1.pdb).
When writing a PDB file, tleap has a lot more information available than
when it is reading one. Basically, it knows where all the bonds are in
the system, and hence can check if there is a bond between two residues,
and consider adding a TER card if there is no bond.
When reading a PDB file, such information is not available.
While it is possible that tleap might be modified to recognize your
particular example, I wouldn't hold my breath. I'm moderately familiar
with many parts of that code, and I wouldn't have a clue about how to
even design a fix. And, it might well break other use cases, where the
user deliberately removed the TER cards, and would be upset if tleap
tried to over-ride that decision.
In any case, you now have a simple workaround, which also makes your
receptor.pdb file more compliant with the PDB standard.
....dac
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Received on Thu Dec 06 2018 - 06:00:02 PST
