On Tue, Aug 18, 2020, Ayesha Fatima wrote:
>FATAL: Atom .R<CASP 615>.A<HN 14> does not have a type.
The PDB/IUPAC/Amber name for these atoms is "H", not "HN". Easiest thing is
to use a text editor or simple script to change the name.
>Prior to this I used the propka server to detect the protonation states for
>HIS. the output .pqr has funny atoms like
>
>ATOM 23 HG22 THR 20 90.084 66.680 49.259 0.0642 1.4870
>ATOM 24 HG21 THR 20 89.664 66.662 47.680 0.0642 1.4870
>ATOM 25 HB THR 20 90.620 68.783 48.034 0.0043 1.3870
>ATOM 26 HG23 THR 20 91.022 65.897 48.173 0.0642 1.4870
Why do you think these names are "funny"? I don't see any problems. Does
tleap not like them? (Are you sure this is related to propka? THR doesn't
have any alternate protonation states.)
You can look at the $AMBERHOME/dat/leap/lib/amino12.lib (or similar files) to
see the names of all atoms in protein residues.
....dac
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Received on Tue Aug 18 2020 - 05:30:02 PDT
