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>> 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>


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

========================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to