Hi All,
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?
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)? or are they the atom # from which they
appear in the pdb file?
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.
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?
I know I'm likely raising a lot of more complicated questions... but if I
just wanted to get a basic idea of this thing in water.. I'm blocking on
the best way to just generate a pseudo-reasonable set of parameters.
Any help would be appreciated.
Thanks,
Jonathan
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Received on Tue Sep 15 2015 - 10:30:02 PDT
