[gmx-users] Re: PRODRG server
Lucio Ricardo Montero Valenzuela
lucioric at ibt.unam.mx
Mon Oct 18 18:18:51 CEST 2010
The message says that you have atoms with the same name. Give each atom an
unique name and try running it again. If you have still trouble, try specifying
explicitly the protonation states.
Hope it helps.
Lucio.
Mensaje citado por "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>
> mohsen ramezanpour wrote:
> > 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 dava at davapc1.bioch.dundee.ac.uk
> <mailto: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 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?
> >
>
> Sounds like the PRODRG server is having issues. Try contacting the PRODRG
> developers directly. You won't be able to get sufficient support on this
> forum.
>
> -Justin
>
> >
> > PRODRG> Normal program end
> >
> >
> >
> > On Sat, Oct 16, 2010 at 4:04 PM, Justin A. Lemkul <jalemkul at vt.edu
> > <mailto:jalemkul at 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.mohsen at gmail.com
> > <mailto:ramezanpour.mohsen at gmail.com>
> > <mailto:ramezanpour.mohsen at gmail.com
> > <mailto: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
> > <mailto:dava at davapc1.bioch.dundee.ac.uk>
> > <mailto:dava at davapc1.bioch.dundee.ac.uk
> > <mailto: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
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------
> >
> >
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
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> > <mailto:gmx-users at gromacs.org>
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> >
> >
>
> --
> ========================================
>
> 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 at gromacs.org
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--
Lucio Ricardo Montero Valenzuela
Estudiante de doctorado en Ciencias Bioquímicas
Lab. del Dr. Federico Sánchez
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210
Mexico
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