Dear Lachele,
Thank you for your help, I solved the problem. I have a simple question, in
tleap.log file almost for all the residues I can see "(Residue 2: ILE,
Nonterminal, was not found in name map.)" But in leap itself (from
terminal), I could not see this sentence. I found in the previous mailing
list, people have similar questions. Should I do something or I don't need
to worry about this?
Thank you,
Rui
On Tue, Nov 26, 2019 at 10:08 PM Lachele Foley <lf.list.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Wed Nov 27 2019 - 08:00:02 PST
