Dear justin no,I had not done it. But this two warning are not present in other my molecules,for example I tested another molecule but the massage was:
defaults to zero instead of generating an error PRODRG> PRODRG> 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 H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: deleted hydrogen H from your input. PRODRG> WARNING: duplicate atom name F . PRODRG> WARNING: duplicate atom name C . PRODRG> WARNING: atoms with same name found. Auto-renaming. PRODRG> Molecule complexity index: 2.09. PRODRG> 2 explicit hydrogen(s) added. PRODRG> 25 bonds 4 ambiguous PRODRG> 36 bond angles 20 ambiguous PRODRG> 18 improper dihedrals 0 ambiguous PRODRG> 7 dihedrals 2 ambiguous PRODRG> 7 partial charges 4 ambiguous PRODRG> Net charge on molecule: 0.000 PRODRG> Using charge groups. PRODRG> Writing GROMACS topology. PRODRG> GROMACS topology quality on 0-10 scale: 5.7 GENDRG> Best structure was iteration 931 with 7.66034174 PRODRG> Spawning GROMACS version 3.3.3... PRODRG> RMSD from GROMOS bond ideality (Angstrom) : 0.019 PRODRG> RMSD from GROMOS angle ideality (degrees) : 2.332 PRODRG> RMSD from GROMOS plane ideality (degrees) : 1.169 PRODRG> Number of improper improper dihedrals : 0 PRODRG> RMSD from starting bonds (Angstrom) : 0.036 PRODRG> RMSD from starting angles (degrees) : 3.155 PRODRG> RMSD from starting planes (degrees) : 1.494 PRODRG> RMSD from starting coords (Angstrom) : 1.930 PRODRG> Writing: SCRHWMMPG Unfortunately PRODRG crashed beside I have done these 6 month ago.exactly with this molecules and I could recieve zip files from server. but I can not do the same action with the same files?what do you think? PRODRG> Normal program end On Sat, Oct 16, 2010 at 4:04 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > These error messages are likely more important: > > > PRODRG> WARNING: multiplicity of generated molecule is not 1. > PRODRG> WARNING: bond type assignment failed at C13 > > There is something about the chemical structure involving this atom that > PRODRG can't handle. Based on the information you've provided, however, > there's no real way anyone can give you much advice. Have you tried drawing > the molecule with the JME editor provided by PRODRG instead of using a .pdb > file? > > -Justin > > mohsen ramezanpour wrote: > >> actually the final massage was :Unfortunately PRODRG crashed >> >> On Sat, Oct 16, 2010 at 11:36 AM, mohsen ramezanpour < >> ramezanpour.moh...@gmail.com <mailto: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 <mailto: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 >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 >
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