Have you ever tried pdbfixer? It'll build-in missing loops via simple
geometrical arcs.
If you don't care about the physicality at the gaps (outside of not wanting
terminal charges), you could always let tleap build the ridiculous bond
then use ParmEd's `deleteBond` to remove that stretched bond (and all other
valence terms that run through it). You'd probably want some kind of
restraint to prevent the caps from going all over the place, but such an
approach is likely easy enough to automate.
All the best,
Jason
On Fri, Oct 15, 2021 at 1:53 PM Brian Radak <brian.radak.gmail.com> wrote:
> I presume you are only recommending dangling ends for density fitting,
> not simulation. Unfortunately I'm looking to prepare a ligand-protein
> complex for a binding free energy calculation, so dangling ends are no
> good, as are strong charged interactions with termini.
>
> I did notice the gap detection in pdb4amber, although most deposited
> PDBs have a list of missing residues already, so this is not a huge time
> saver. I played around with ParmEd for a bit trying to insert new
> atoms/residues for the caps, but it was hopelessly difficult when the
> insertion is in the middle of a chain (you have to re-index the residues
> or else split the chain and then re-combine - just not good).
>
> I'm just surprised, bc this is ridiculously easy in CHARMM/XPLOR with
> residue patching, even if the resulting capped residue is non-standard.
>
> Cheers,
>
> Brian
>
>
> On 10/14/21 9:19 PM, David A Case wrote:
> > On Thu, Oct 14, 2021, Brian Radak wrote:
> >
> >> Is there a script in AmberTools that automates insertion of capping
> >> groups
> >> (e.g., ACE and NME) along with TER characters when prepping a PDB for
> >> tleap, etc.? I was kind of shocked when the manual suggested doing
> >> this by
> >> hand as the obvious way. Would this be an attractive feature in
> >> pdb4amber
> >> or are there simply enough third party preparation tools available on an
> >> academic license?
> >
> > pdb4amber will tell you where the gaps are, but does not impose any
> > particular
> > way to handle them. I've never used ACE/NME in this situation, but
> > that is
> > just me. What phenix (and I) do with gaps is to use pdb4amber to find
> > the
> > gaps, then just add a deleteBond command to the tleap script to remove
> > the
> > bond that tleap creates during the loadPdb command. This leaves dangling
> > ends, but that is not an obvious problem for molecular mechanics force
> > fields. No need for TER cards in any pdb file, although they will
> > appear if
> > you later use ambpdb with the final prmtop file as input.
> >
> > Maybe others on the list have a more sophisiticated workflow here.
> >
> > ....dac
> >
> >
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Jason M. Swails
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Received on Mon Oct 18 2021 - 08:00:02 PDT
