Dear Tainah,
you may try the command loadPdbUsingSeq in tleap (cf page 233 Amber
manual): If the sequence you define your peptide with lacks the explicit
terminal residue names like NALA or CGLY, all peptide residues are
defined as mid-chain residues, i.e. the terminal ones are not
automatically converted to the standard terminal species (NH3+ or COO-).
After that, you manually add a bond between the first N and the last
C(=O), (bond command in tleap) and you are done.
Since the bond command simply depends on the length of the peptide, the
tleap input could be created via an external script.
(This general approach for cyclic peptides worked for me in earlier
Amber versions; I did not test it explicitely in Amber20, though.)
In your case, where you also have an additional ligand in your pdb file,
I'm not sure about the tleap logic: if you simply add your ligand's
residue name to the sequence list, tleap might try to form a bond
between the last residue (being a "mid-chain" still) and your ligand,
which won't work and is not what you want, of course. But maybe tleap
recognizes the missing valency in the ligand and does not try to form a
bond there.
Alternatively, you could read in your peptide from one file and your
ligand into a second UNIT from a second pdb file via loadPdb, and then
use tleap's combine command to create a new unit, which may be saved.
Maybe that helps...
Best Regards,
Anselm
[NHR.FAU]
On 04/15/2021 12:34 PM, Tainah Dorina Marforio wrote:
> Hello!
> I'm working on complexes made of a cyclic peptide (the receptor) & a ligand.
> To obtain the receptor, I create the amino acid sequence with tleap and I make the bond between N and C. Then I save the parm7 & rst7 and run a minimization. Everything works fine. Then I take the cyclic minimized structure and create a pdb with ambpdb (let's call it min.pdb) I manually create the complex on min.pdb, obtaining the complex.pdb (with TER and END in the right places).
>
> To obtain the parm7 & rst7 of the complex, on leap I call the forcefields that I need (ff14SB, gaff, water.tip3p) and load the frcmod/prepi for the ligand. As soon as I load the complex.pdb, leap adds the hydrogens to the nitrogen (to make the NH3+) and OXT (for COO-).
>
> Is there any way to avoid leap adding these "missing atoms" to standard residues?
>
> * Since I have loooots of cyclic peptides to work with, I would like to avoid passing trhough xleap and do edit, delete/draw bond, and especially, I would like to avoid to modify manually the atom type/name in the xleap table.
> Also, I would like to avoid to parameterize all the cyclic peptides as non-standard residues.
>
> Thank you
>
> Tainah
>
>
>
>
>
>
>
> Tainah D. Marforio
>
> Post-Doc Fellow
> <http://www.site.unibo.it/nanobio-interface-lab/en>Dipartimento di Chimica "Giacomo Ciamician"
> Alma Mater Studiorum - Università di Bologna
> Via Selmi 2, 40126 Bologna - Italy
> www.unibo.it/sitoweb/tainah.marforio2<http://www.unibo.it/sitoweb/tainah.marforio2>
> www.site.unibo.it/nanobio-interface-lab/en<http://www.site.unibo.it/nanobio-interface-lab/en>
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Received on Thu Apr 15 2021 - 17:30:02 PDT
