[gmx-users] Re: PRODRG server

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Sat Oct 16 16:16:11 CEST 2010 

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
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 <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>>
>> 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>
>>
>>
>>
>>    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
>
> ========================================
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