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 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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