Maybe there are more efficient ways, but I usually add the capping atoms
to the pdb (using Chimera or Avogadro, for example)
and then change the residue name of those atoms to "ACE". Then tleap
should recognize the residue and add the hydrogens.
hope this helps,
David.
On Fri, Apr 10, 2020 at 1:10 AM Lod King <lodking407.gmail.com> wrote:
> thanks a lot.
>
> When AMBER is creating prmtop file for my protein. Do I have to prepare
> some steps to rename in the PDB file prior to call AMBER, or it will
> automatically add the ACE to my peptide?
>
> On Thu, Apr 9, 2020 at 10:02 PM David Sáez <davidsaez.udec.cl> wrote:
>
> > Hi Lod,
> >
> > I guess that piece of text refers to the charge derivation procedure for
> > residues that would normally be part of a bigger molecule or polymer.
> >
> > For example, in deriving RESP charges for an aminoacid residue you cannot
> > use the zwitterionic or neutral molecule, because in an actual protein
> > that residue has "lost" some of the atoms in the formation of the peptide
> > bond. So the standard is, for charge calculation purposes,
> > to block the residue with NME and ACE residues at the C-terminal and
> > N-terminal groups, respectively. In that way I think you give a common
> > "peptide-like" environment to all your residues.
> >
> > Then you make the QM calculations on that blocked structure, and in the
> > charge derivation process you keep the charges fixed to a standard value
> > for those blocking groups,
> > varying only the atomic charges of your actual residue.
> >
> > The procedure is nicely explained in this tutorial,
> > https://ambermd.org/tutorials/advanced/tutorial1/section1.htm, for a
> > non-protein molecule.
> >
> > Best,
> >
> > David.
> >
> > On Thu, Apr 9, 2020 at 11:47 PM Lod King <lodking407.gmail.com> wrote:
> >
> > > Hi Amber
> > >
> > > *I have seen many papers talking about *"acetylated the truncated N-
> > > terminal ....... to eliminate artificial charges at the N-termini"
> > >
> > > *I wonder what does it mean to the PDB structure and how did it
> achieve?
> > *
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Received on Thu Apr 09 2020 - 23:30:02 PDT
