Well, there is another issue at hand which further complicates the issue of running things through antechamber - the library files im using are a set of rotamers which need to stay in their specific conformations, this would basically mean I need to re-optimize 200 or so rotamers through antechamber, and there is no guarantee that while running them through antechamber they will remain in their specific conformations... Not such a facile task.
Anywho, this no longer poses the same problem it once did - the program I have made to modify the amber atom types in the tleap mol2 files to elemental atom types seems to allow OpenBabel to interpret the mol2 files with the single-bond connectivity. I do not need exact connectivity, just the basic skeleton of the structure.
Once I've manipulated the molecule through OpenBabel, I'm running it back through tleap (using OB to output the structure into pdb) so leap is able to correctly interpolate the output via the rotamer library .off files. It's a little complicated to explain, but everything is OK.
Thanks all for the help!
Nick
________________________________________
From: Hannes Loeffler [Hannes.Loeffler.stfc.ac.uk]
Sent: 20 March 2014 10:07
To: AMBER Mailing List
Cc: Browning, Nicholas
Subject: Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
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 - 04:00:03 PDT
