Re: [AMBER] Automated capping of missing loops?

From: Brian Radak <>
Date: Fri, 15 Oct 2021 13:52:48 -0400

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.



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 Fri Oct 15 2021 - 11:00:02 PDT
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