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 Sat May 31 2014 - 08:00:02 PDT
