Hello,
I am using tleap to prepare a protein/ligand complex. It seems like tleap
doesn't understand the complex PDB file (I attached the file here). I think
there is something wrong with the connection. Can I manually delete all the
connections in the PDB file? There are glycans (0YB) in my system, now
tleap doesn't understand the connections between all the glycans and the
Asparagines (the asparagines connected to glycans are named as NLN).
Previously when I prepare for the ligand alone, I used "bond" command to
generate all the glycan/NLN connections by myself. I think as for the
complex, I should do the same thing. Do you have any suggestion to solve
this problem? Thank you.
Errors:
"> complex = loadpdb 6058_pose1.pdb
Loading PDB file: ./6058_pose1.pdb
Created a new atom named: HD2 within residue: .R<NLN 19>
Created a new atom named: HD2 within residue: .R<NLN 55>
Created a new atom named: HD2 within residue: .R<NLN 64>
Created a new atom named: HD2 within residue: .R<NLN 152>
Created a new atom named: HD2 within residue: .R<NLN 173>
Created a new atom named: HD2 within residue: .R<NLN 177>
Created a new atom named: HD2 within residue: .R<NLN 192>
Created a new atom named: HD2 within residue: .R<NLN 198>
ERROR: Comparing atoms
.R<0YB 210>.A<C2 19>,
.R<0YB 210>.A<H1 2>,
.R<0YB 210>.A<O5 3>, and
.R<0YB 209>.A<C1 1>
to atoms
.R<0YB 210>.A<C2 19>,
.R<0YB 1>.A<C1 1>,
.R<0YB 210>.A<O5 3>, and
.R<0YB 209>.A<C1 1>
This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named C1 from 0YB did not match !
!
!ABORTING.
"
Best regards,
Rui
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Received on Tue Nov 26 2019 - 18:00:01 PST
