[gmx-users] Re: PRODRG server

[Justin A. Lemkul]

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
> 
>     	  	
> 
>     ------------------------------------------------------------------------
> 
> 

-- 
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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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