Thank you very much.
On Thu, Apr 9, 2020 at 11:11 PM David Sáez <davidsaez.udec.cl> wrote:
> 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
