Hi,
ideally you would be using antechamber but strangely (but it should!)
it doesn't perceive bond orders in the absence of bonds in the mol2. If
you have bond orders in the mol2 already you may be able to use
antechamber with -j 4 and -at sybyl (for SYBYL types, assuming the
current types are GAFF) but I have seen this fail in some cases, i.e.
unsuitable assignment.
The mol2 reader in Openbabel doesn't know about types other than Sybyl
though it can assign GAFF types internally.
Tleap would essentially need code from antechamber to be able to assign
things like bond order and atom types.
Cheers,
Hannes.
On Tue, 18 Mar 2014 14:59:47 +0000
"Browning, Nicholas" <nicholas.browning08.imperial.ac.uk> wrote:
> Dear All,
>
> Having a great deal of trouble trying to find a workaround to this
> issue. It's been posted about before and it's been deemed unecessary
> to fix, however I feel this bug is something that needs attending to.
>
> 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).
>
> If anyone else has encountered this issue and knows of a workaround
> then please let me know! I need to be able to obtain self-sufficient
> mol2 (or any other format with well-defined connectivity/bond-order)
> in order for OpenBabel to be able to interpret structures correctly.
>
> Cheers,
>
> Nick
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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