[gmx-users] PRODRG server

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Sat Oct 16 10:06:44 CEST 2010

Dear gromacs users

I have a pdb file who include protein and a drug.I separated them by pymol
software and saved them separately.now I want to make topology and gro file
for it but
I am facing with this page below.can you guid me?
thanks in advance.

PRODRG> Starting up PRODRG version 071121.0636
PRODRG> PRODRG written/copyrighted by Daan van Aalten
PRODRG> and Alexander Schuettelkopf
PRODRG> Questions/comments to dava at davapc1.bioch.dundee.ac.uk
PRODRG> When using this software in a publication, cite:
PRODRG> A. W. Schuettelkopf and D. M. F. van Aalten (2004).
PRODRG> PRODRG - a tool for high-throughput crystallography
PRODRG> of protein-ligand complexes.
PRODRG> Acta Crystallogr. D60, 1355--1363.
PRODRG> PDB mode detected.
PRODRG> WARNING: deleted hydrogen  H1  from your input.
PRODRG> Molecule complexity index: 2.17.
PRODRG>   1 explicit hydrogen(s) added.
PRODRG>  27 bonds                7 ambiguous
PRODRG>  40 bond angles         18 ambiguous
PRODRG>  19 improper dihedrals   0 ambiguous
PRODRG>   9 dihedrals            5 ambiguous
PRODRG>   5 partial charges      0 ambiguous
PRODRG> Net charge on molecule:   1.000
PRODRG> Using charge groups.
PRODRG> WARNING: multiplicity of generated molecule is not 1.
PRODRG> WARNING: bond type assignment failed at C13  .
PRODRG> Writing GROMACS topology.
PRODRG> GROMACS topology quality on 0-10 scale:  6.2
PRODRG> Keeping old coordinates.
PRODRG> RMSD from GROMOS bond ideality (Angstrom) :   0.038
PRODRG> RMSD from GROMOS angle ideality (degrees) :   2.230
PRODRG> RMSD from GROMOS plane ideality (degrees) :   0.886
PRODRG> Number of improper improper dihedrals     :       0
PRODRG> Normal program end


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