On Wed, Mar 19, 2014, Browning, Nicholas wrote:
>
> What would be a useful fix is for leap to output mol2 files with the
> correct SYBYL style atom types rather than printing out amber atom
> types (Which are not compatible with structures designed to load SYBYL
> atom types...).
But tleap is a part of the Amber tool chain, and Sybyl atom types would mean
that the resulting mol2 files would be of no use to Amber.
One could add a "set default SybylTypes on" flag to tleap, to put get the
desired atom types, but (a) that seems to me to be likely to create lots
of confusion; and (b) there would still be the problem of the bond orders.
Given that there is a simple workaround (running through antechamber) that
provides both Sybyl atom types and bond order assignments, I'm not yet
convinced a change is necessary.
> replace them with their elemental names as a workaround to
> get OB to interpret it correctly (OB can then assign roughly correct
> SYBYL atom types e.g C -> C.3, again based on connectivity).
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.
...dac
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Received on Wed Mar 19 2014 - 19:00:03 PDT
