Re: [AMBER] Parametrization of non-standart residues

From: James Starlight <>
Date: Tue, 3 Jun 2014 14:57:57 +0200


Some methodological question about capping of my residue with ACE and NME
groups, Does it possible to do it quickly using some tleap (not xleap)
script (adding ACE to selected N and NME to C atoms of my non standart
residue keeping initial geometry of it?

2014-05-31 16:53 GMT+02:00 Jason Swails <>:

> On May 31, 2014, at 9:21 AM, James Starlight <>
> wrote:
> > Many thanks for information!
> >
> > I'll try to spend time on RED tutorials before doing my parametrization.
> > However in cases when I need for blank topology of my residue (for
> > qm/calculations for instance) providing explicitly only its bonding to
> the
> > rest of the protein as I understood antechamber parametrization might be
> > enough.
> > Assuming that I'm providing residue with CO in tail and NH in head
> > positions (all atoms corresponds to the complex.pdb) could I provide mol3
> > file (with head and tail specification) to leap to build my complex?
> Indeed, if you plan on treating this residue entirely with QM in a QM/MM
> calculation, the charge derivation scheme does not matter at all. There
> will be no effective difference between antechamber and RED in this case.
> Only the van der Waals parameters are used for atoms in a quantum region.
> Check your PDB file -- does it have TER cards between your custom residue
> and the residues on either side? Certain things in the PDB, like a TER
> line for instance, will trigger leap to terminate one chain and start a new
> one, even if HEAD and TAIL atoms are set.
> See if you can figure out why tleap is terminating chains around your
> residue. The "desc" command will show you what a unit is (it DESCribes the
> unit). So you can look at the unit in tleap to make sure it has the
> properties you expect it to have.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Jun 03 2014 - 06:00:03 PDT
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