[gmx-users] Re: PRODRG server
ramezanpour.mohsen at gmail.com
Sat Oct 16 10:23:44 CEST 2010
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> 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> Writing: SCRHWMMPG
> PRODRG> Normal program end
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