[gmx-users] Re: PRODRG server
Justin A. Lemkul
jalemkul at vt.edu
Sat Oct 16 16:27:16 CEST 2010
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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--
========================================
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
========================================
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