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
========================================
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