[gmx-users] PRODRG atom number limit

[Daan van Aalten]

Hi Hugo

This is not really a GROMACS related question, so perhaps not suitable for
this list, but :

the atom limit can be changed at the compilation stage - if you let us
know what you want we can make this for you (please note however that an
executable with a 300 atom limit already takes up 0.5 GB of memory).

As to the complexity: one of the most time consuming steps in PRODRG is to
find "the longest path" in a molecule, by simply evaluating all possible
paths one can draw in the molecule's 2D structure. This then allows us to
order the connectivity table in a logical way, such that if you input 10
different PDB files of the same molecule with the atoms in different
order (and even with different names), we get a unique "molecular
descriptor" that is useful for database searches etc. etc.
This approach works fine for your average small organic molecule - but
evaluating all possible paths of atoms that cover the entire molecule in,
say, a nanotube is a formidable problem in terms of the number of
possibilities. So there is a "molecular complexity" cut-off that prevents
PRODRG from running for years on a single molecule.
We are currently working on short-cuts to circumvent this problem for
nantubes/bucky balls in particular.

cheers

Daan


On Tue, 23 Mar 2004, hugo verli wrote:

> Hi,
>
> in previous correspondences with this list I indicated my interest in generate
> topologies, using PRODRG server, of big molecules (>100 atoms or even >300).
> So it was indicated to me the local version of PRODRG. However, its appear to
> be a limit of about 300 atoms in the local version, is it correct? But I
> observed not only a atom number limit, but something like a complexity limit,
> because I submit a molecule with about 200 atoms and the following error is
> observed:
>
> ERRDRG> Error in recursion (molecule too complex)
>
> Is there any way to generate these topologies? The size of the molecules is of
> ultimate relevance in the system I am intented to simulate.
>
> Many thanks in advance,
>
> Hugo Verli.
>
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Dr. Daan van Aalten                    Wellcome Trust RCD Fellow / Reader
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Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
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