[gmx-users] Re: PRODRG server

[mohsen ramezanpour]

actually the final massage was :Unfortunately PRODRG crashed

On Sat, Oct 16, 2010 at 11:36 AM, mohsen ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> 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>
> PRODRG> Questions/comments to dava at davapc1.bioch.dundee.ac.uk
>
> PRODRG>
> 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>
> PRODRG>
> 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> Writing: SCRHWMMPG
> PRODRG> Normal program end
>
> best
> Mohsen
>
>
> ------------------------------
>
>
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