actually the final massage was :Unfortunately PRODRG crashed On Sat, Oct 16, 2010 at 11:36 AM, mohsen ramezanpour < ramezanpour.moh...@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 d...@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 > > > ------------------------------ > >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
