Thanks!
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 <jason.swails.gmail.com>:
>
> On May 31, 2014, at 9:21 AM, James Starlight <jmsstarlight.gmail.com>
> 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
