actually the final massage was :<font size="5">Unfortunately PRODRG crashed</font><br><br><div class="gmail_quote">On Sat, Oct 16, 2010 at 11:36 AM, mohsen ramezanpour <span dir="ltr"><<a href="mailto:ramezanpour.mohsen@gmail.com">ramezanpour.mohsen@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear gromacs users<br><br>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 <br>
I am facing with this page below.can you guid me?<br>
thanks in advance.<br><table><tbody><tr><td><pre>PRODRG> Starting up PRODRG version 071121.0636<br>PRODRG> PRODRG written/copyrighted by Daan van Aalten<br>PRODRG> and Alexander Schuettelkopf<br>PRODRG> <br>PRODRG> Questions/comments to <a href="mailto:dava@davapc1.bioch.dundee.ac.uk" target="_blank">dava@davapc1.bioch.dundee.ac.uk</a><br>
PRODRG> <br>PRODRG> When using this software in a publication, cite:<br>PRODRG> A. W. Schuettelkopf and D. M. F. van Aalten (2004).<br>PRODRG> PRODRG - a tool for high-throughput crystallography<br>PRODRG> of protein-ligand complexes.<br>
PRODRG> Acta Crystallogr. D60, 1355--1363.<br>PRODRG> <br>PRODRG> <br>PRODRG> PDB mode detected.<br>PRODRG> WARNING: deleted hydrogen H1 from your input.<br>PRODRG> Molecule complexity index: 2.17.<br>
PRODRG> 1 explicit hydrogen(s) added.<br>PRODRG> 27 bonds 7 ambiguous<br>PRODRG> 40 bond angles 18 ambiguous<br>PRODRG> 19 improper dihedrals 0 ambiguous<br>PRODRG> 9 dihedrals 5 ambiguous<br>
PRODRG> 5 partial charges 0 ambiguous<br>PRODRG> Net charge on molecule: 1.000<br>PRODRG> Using charge groups.<br>PRODRG> WARNING: multiplicity of generated molecule is not 1.<br>PRODRG> WARNING: bond type assignment failed at C13 .<br>
PRODRG> Writing GROMACS topology.<br>PRODRG> GROMACS topology quality on 0-10 scale: 6.2<br>PRODRG> Keeping old coordinates.<br>PRODRG> RMSD from GROMOS bond ideality (Angstrom) : 0.038<br>PRODRG> RMSD from GROMOS angle ideality (degrees) : 2.230<br>
PRODRG> RMSD from GROMOS plane ideality (degrees) : 0.886<br>PRODRG> Number of improper improper dihedrals : 0<br>PRODRG> Writing: SCRHWMMPG<br>PRODRG> Normal program end<br><br>best<br>Mohsen<br>
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