On Tue, Mar 18, 2014, Browning, Nicholas wrote:
>
> Strictly speaking, mol2 files should be self-sufficient
> units which can be plugged into other tools for
> visualisation/modification/simulation. The format of the mol2 file
> output from leap is incorrect, both in terms of how it deals with
> connectivity (double/triple bonds labelled incorrectly as single bonds)
> and how it labels atoms (enters data other than the standard SYBYL atom
> types). This means that mol2 files are only useable for amber, which is
> giving me a lot of trouble (I am using the c++ OpenBabel distributable
> for atomic modifications).
I think that both problems can be solved by sending the mol2 file that
tleap creates through antechamber:
antechamber -fi mol2 -i <tleap-created-file> -fo mol2 -o <new-mol2-file> -at
sybyl
This should give you Sybyl atom types and at least a good shot
at correct bond orders. But there are clear limitations here:
a. You need a good geometry, since antechamber infers bonding from geomtry
b. It's not well tested: Amber doesn't care about bond orders, and only
has the option of Sybyl atom types for people like you who seem to
require them
Still, it seems worth a shot.
> Since I am loading the .off files into leap prior to loading a mol2/pdb
> structure, surely leap would now have both bonding and atom type information
> since these are contained within the lib files?
Sure, but these are *Amber* atom types and bond orders. You seem to be
needing something different.
...dac
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Received on Tue Mar 18 2014 - 10:00:02 PDT
