[gmx-users] PRODRG problem

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Wed Jan 23 13:11:17 CET 2002

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> Starting up PRODRG version 050901
PRODRG> PRODRG written/copyrighted by Daan van Aalten
PRODRG> Questions/comments to dava at davapc1.bioch.dundee.ac.uk
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> 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.

Alexandre Suman de Araujo
IFSC - USP - São Carlos
UIN: 6194055

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