Dear Jonathan,
we recently created a small parameter set for isopeptide bonds, i.e.
modified residues of Asp/Asn, Glu/Gln, and Lys that have a third valency
for a peptide bond similar to the CYX residue for disulfide bonds.
Using the R.E.D. methodology, a set of charges (for terminal and
mid-chain residues) was derived, which was incorporated into ff99SB and
ff14SB parameter sets. In a current project, we are using the ff99SB
force field.
If you are interested in the parameter set, please contact me off the
list for technical details, as the work is not yet published.
Regards,
Anselm
Am 15.09.2015 21:55, schrieb Jonathan Gough:
> The one followup question I have is...
>
> Thy cyclic peptide has an un-natural bond. An Internal LYS.NZ--ASP.CG amide
> bond.
>
> leap (as far as I can tell) made the bond. However, ff14SB doesn't have the
> requisite bond/angle/torsion parameters for the non-native LYS-ASP amide
> bond. (hence why I was asking about needing to make a new residue). At the
> most basic level it's just an aliphatic amide bond, is there a way to
> import these from gaff yet retaining the rest of the ff14SB parameters?
>
>
>
> 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 Thu Sep 17 2015 - 00:30:03 PDT
