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 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 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 <jalem...@vt.edu
<mailto: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>
<mailto: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>
<mailto: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 <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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