Dear Brian,
In general I use Pymol (Builder) or VMD (Molefacture) to add ACE/NME caps to the structure before going through the AMBER workflow...
Particularly, Pymol may help you finding a proper rotamer in the case it is relevant for your system...
If you are very lazy or the system is very big/complex, you can modify the PDB by copying the "O" ATOM record from the Ct residue, renaming it to "N NME", increasing the resid by 1, changing X, Y or Z by (let say) 1-2 A, and letting LEAP to complete the missing atoms... The minimization will hopefully fix any structural issue... (a similar strategy can be use for ACE and Ct)
Hope it helps,
Matías
----- Mensaje original -----
De: "Brian Radak" <brian.radak.gmail.com>
Para: amber.ambermd.org
Enviados: Viernes, 15 de Octubre 2021 14:52:48
Asunto: Re: [AMBER] Automated capping of missing loops?
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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Received on Sun Oct 17 2021 - 13:30:02 PDT
