AMBER: RE: Tutorial5 -- sustiva and xleap

From: Ross Walker <>
Date: Thu, 6 Sep 2007 06:20:08 -0700

Dear Domanski,

For more general questions, rather than specific problems with the
tutorials, it is better to mail questions to the Amber mailing list. See for details on how to sign up. This way the
messages go into the archive of this reflector to help other users.

> I am relatively new to AMBER, antechamber and Co., so, I use
> your (very
> good!) tutorials as a start point for my own studies. And there is one
> point not so clear for me. If one considers the structure of
> sustiva, one
> can see aromatic rings and multiple bonds in the molecule
> (sustiva_2d.gif). But I can't recognize any of the multiple
> bonds on the
> screenshot from the xLeap (xleap_gaff4.jpg). Is the
> information about bond
> multiplicity lost through the conversion to "prepi" format?
> Or is it just
> hidden?

There really isn't a concept of multiple bonds in the Amber force field. All
bonds are treated with the same harmonic potential. The difference would be
that a double bond has a higher force constant than a single bond. Thus all
that actually matters in terms of the topology is that a bond exists and
that the atom types are appropriate. Thus leap does not draw in
double/triple bonds etc.

> If I load a "mol2" file into [xt]Leap, I see multiple bonds,
> but not if I
> load a "prepi" file. Does it mean the "mol2" is better than "prepi"?

It is actually possible to set bond valencies in leap such that it draws in
double bonds etc in the edit window, this information exists in a mol2 file
but not in a prepi file. However, this is purely cosmetic and has no effect
on the resulting topology / parameters etc. So short answer is don't worry
about it.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Sun Sep 09 2007 - 06:07:18 PDT
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