Hi!
For Thanksgiving-related reasons I can't spend lots of time on this
right now, but...
This sort of error usually happens when too many bonds happen
somewhere. Maybe you missed a "TER" card somewhere or maybe have an
extra bond command, etc. I would carefully check all the bonding and
TER cards.
On Tue, Nov 26, 2019 at 8:52 PM Rui Chen <rchen6.ualberta.ca> wrote:
>
> 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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Nov 26 2019 - 21:30:02 PST
