[MMTK] Cant read full-atom RNA PDB file

Anna Gorska gvalchca.agr at gmail.com
Wed Jul 9 12:23:22 UTC 2014


Dear all,
is there any way to analyse the full atom (meaning with the hydrogens) PDB file and the dcd trajectory?
It works only if I let MMTK guess positions of my hydrogens, but when I try to read it full this is the error I get:

IOError: Atom H5' of PDB residue RG not found in residue RG5 of object C.RG5_1

As if the Charmm naming scheme is storage to MMTK or it was lacking the data for 3/5 ters of RNA,

Do you have any idea ?

Regards,

Anna Gorska
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