On Thu, 20 Mar 2014 09:47:04 +0000
"Browning, Nicholas" <nicholas.browning08.imperial.ac.uk> wrote:
> I just find it a little strange that leap offers to produce mol2
> files (which are a standardised file format and widely used by other
> simulation, graphical and modification toolsets), yet does not
> conform to the intended file format. However if leap does not load
> any information regarding explicit bond order, then naturally this is
> understandable.
>
> > We *should* have tleap populate the element columns in the pdb
> > files it outputs. Then OB could presumably do a pdb -> mol2
> > conversion without any need to change atom names.
>
> This works great for standard residues, but when using non-standard
> residues OpenBabel has no way of knowing how to connect each atom
> other than based on distances, which can often produce incorrect
> connectivity. I've not yet found a structure that allows you to
> specify non-standard residue connectivity (similar to leaps .off file
> system) for reading PDBs.
PDBs can have CONECT records and OB's PDB reader would read them and
assign bonds accordingly. I believe tleap doesn't write these records
but antechamber does.
> I did not realise antechamber was capable of assigning correct bond
> orders - is there an example available which I can follow which
> applies to my situation of using non-standard residues /w PDB?
It is the very purpose of antechamber to assign bond orders. You may
want to have a look through the AMBER tutorials.
--
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Received on Thu Mar 20 2014 - 03:30:02 PDT
