Re: [AMBER] Parametrization of non-standart residues

From: Parker de Waal <>
Date: Tue, 3 Jun 2014 13:15:30 +0000

Hi James,

Unfortunately leap cannot build atoms that it doesn't know about. Unlike the automatic capping N and C terminal residues for an entire protein, capping a custom residue will require you to add the ACE and NME groups manually or through another program.

For my ligand and residue building I use the freely available MarvinSketch followed by geometry optimization and RESP charge calculations using the R.E.D. server.


-----Original Message-----
From: James Starlight []
Sent: Tuesday, June 03, 2014 8:58 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Parametrization of non-standart residues


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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