Re: [AMBER] loading molecule in xleap and saving it in mol2 format

From: Hannes Loeffler <>
Date: Fri, 20 Mar 2015 10:37:29 +0000

On Fri, 20 Mar 2015 11:14:19 +0100
FyD <> wrote:

> > I mean in general, this stars are not there in
> > the mol2 file but is it ok in my case?
> Yes - each program adapts the mol2 file format; same 'problem' with
> the PDB file format...

The four asteriks are place holders for non-optional fields. None of
the fields leap filled in in this case are, so they are actually

The PDB format is as it is. It just has been much abused for purposes
it was not originally designed for. If it had only been used as a
read-only format...

> > Moreover, is partial charges are listed in the last column?
> Yes

No. Charges are the 9th _field_ and are optional. The last and
10th, obviously also optional, field are status bits which are probably
only relevant to Sybyl. The mol2 format is not a column format.


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Received on Fri Mar 20 2015 - 04:00:02 PDT
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