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 - 12:30:03 PDT
