Very helpful,
Thanks David!
On Tue, Sep 15, 2015 at 3:02 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Sep 15, 2015, Jonathan Gough wrote:
> >
> > I would like to simulate a (bi)cyclic peptide and I was wondering if
> anyone
> > had any suggestions on how best to do parameterize/build this using
> > (mostly) ff14SB via leap.
> >
> > I see from the List that one can simply make an alternate leaprc.ff14SB
> > file that is absent of the terminal residues and then just draw a bond
> > between the N and C terminus.
> > http://archive.ambermd.org/201303/0171.html
> >
> > 1. Is this the best way to do it?
>
> It's how I would proceed. That would create a cyclic peptide, not a
> bi-cylcic
> one, however.
>
> >
> > 2. Can anyone provide an explanation of how "atoms" are defined in leap?
> > Are they simply the variable given to the pdb dot residue# dot atom name
> > (as per the manual trx.32.SG)?
>
> Yes. Use the "desc" command in tleap if you are uncertain about exactly
> how
> LEaP is internally designating its atoms.
>
> >
> > 3. Within the peptide, I have an internal peptide(amide) bond LYS.NZ --
> > ASP.CG. I understand i can use the bond command to create said bond,
> but is
> > there a way to turn off the add missing atom function in leap? I can't
> seem
> > to find a command to deleteAtom in leap.
>
> It's called "remove"; use the "help remove" command in tleap to see the
> syntax. (I generally use the graphical editor in xleap to add bonds
> and remove atoms, but that is just a personal preference; the corresponding
> commands are in tleap as well. Depends on how often you need to do this,
> and
> how long it takes you to grok the tleap syntax involved.)
>
> >
> > If I used gaff/antechamber to create a "new residue," I'm having a hard
> > time wrapping my head around how to do it, would it be a single residue
> > that appears 2x in the PDB? or would I just need to run the entire
> > bi-cyclicpeptide through antechamber?
>
> It doesn't seem to me like this is a project that needs to be creating a
> "new
> residue". Once you have removed the unwanted atoms and created the new
> bonds,
> you could use saveOff within tleap to save the result. This would be
> useful,
> for example, if you then wanted to simulate binding of this cyclic peptide
> to a receptor (say).
>
> ...hope this helps...dac
>
>
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Received on Tue Sep 15 2015 - 12:30:05 PDT
