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>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 15 2021 - 04:00:02 PDT
