[gmx-users] Re: PRODRG atom number limit

Ing. Vojtěch Spiwok Vojtech.Spiwok at vscht.cz
Wed Mar 24 09:01:01 CET 2004

> Hi,
> in previous correspondences with this list I indicated my interest in
> topologies, using PRODRG server, of big molecules (>100 atoms or even
> So it was indicated to me the local version of PRODRG. However, its appear
> 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
> because I submit a molecule with about 200 atoms and the following error
> 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.

I had a similar problem with disubstrate-like drug linked by alkyl chain. I
topologies of both parts by PRODRG, I renumbered the second molecule and
then I cocatenated them by changing of terminal CH3 to CH2, adding the
CH2-CH2 bond, two angles, couple of pairs and dihaedrals etc. I do not know
if this could be applied on your system.

Vojtech Spiwok
ICT Prague

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