[gmx-users] PRODRG problem

[Daan van Aalten]

Hi Alex

The version that's on the server right now can only deal with compounds
of which the number of : atoms, bonds, bond angles, torsion angles should
EACH by < 100 (you have 112 bond angles).
This has in principle nothing to do with PRODRG but with GROMOS where
these limitations exist for topology building blocks (equiv. of .rtp file
in GMX). However, I now have a version which does all the EM etc in GMX
and that deals currently with < 300 atoms. The problem is that rasmol
(which I use to get the little movie on the PRODRG output page) cannot
work with "residues" > 200 atoms or so, so I'm fixing that, too. By the
end of the week there will be a test version of the server so please try
your compound then!

cheers

Daan

On Wed, 23 Jan 2002, Alexandre Suman de Araujo wrote:

> When somebody ask for everything about small molecules here, the answer is:
> "Try to use PRODRG program". I tried to use it with a molecule with 72 atoms
> and I get this error:
> 
> PRODRG>
> PRODRG>
> PRODRG> Starting up PRODRG version 050901
> PRODRG> PRODRG written/copyrighted by Daan van Aalten
> PRODRG>
> PRODRG> Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> PRODRG>
> PRODRG> When using this software in a publication, cite:
> PRODRG> D.M.F. van Aalten, R. Bywater, J.B.C. Findlay,
> PRODRG> M. Hendlich, R.W.W. Hooft and G. Vriend,
> PRODRG> PRODRG, a program for generating molecular topologies
> PRODRG> and unique molecular descriptors from coordinates
> PRODRG> of small molecules.
> PRODRG> Journal of Computer Aided Molecular Design (1996), 10, 255-262.
> PRODRG>
> PRODRG>
> PRODRG> Invalid command line argument: WAT
> PRODRG> PDB mode detected.
> PRODRG>  72 atoms read.
> PRODRG> At least one 6-membered ring detected.
> PRODRG>   0 hydrogens added
> PRODRG>  76 bonds               16 ambiguous
> PRODRG> 112 bond angles         52 ambiguous
> PRODRG>  48 improper dihedrals   0 ambiguous
> PRODRG>  32 dihedrals           12 ambiguous
> PRODRG>  12 partial charges      7 ambiguous
> PRODRG> Net charge on molecule :   0.000
> PRODRG> Writing GROMOS topology
> PRODRG> Writing GROMACS topology
> ERRDRG> Molecule too large for a GROMOS87 topology.
> PRODRG> Drug topology not made, sorry!
> 
> And in it's initial page is write it can work with no more than 100 atoms,
> then I think it can work with 72 atoms.... or not???
> Somebody can say me what is happening???
> 
> Thank you very much.
> 
> []'s
> Alexandre Suman de Araujo
> IFSC - USP - São Carlos
> UIN: 6194055
> 
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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

        O     C           O     C         Visit the PRODRG server to take 
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O   
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "         
       O