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Separated by 3 bonds (except pairs of hydrogens). Pair interactions are generated for all pairs of atoms which are Means that interactions between atoms connected by at most 3 bonds areĮxcluded. Gmx pdb2gmx sets the number exclusions to 3, which It is possible to put more than one dihedral on a rotatable bond. When the field is used, no other dihedrals willīe generated for the bonds corresponding to the specified dihedrals. Gmx pdb2gmx automatically generates one properĭihedral for every rotatable bond, preferably on heavy atoms. Gmx pdb2gmx automatically generates all angles, This is used for the GROMOS96 forcefield. Instead of parameters a string can be added for each bonded interaction, This should only be used in special cases. These parameters override the standard parameters in the itp files. Parameters can be added to bonds, angles, dihedrals and impropers, Optionally bonds, angles dihedrals and impropers. Interactions and residue entries, which consist of atoms and The file contains the default interaction type for the 4 bonded To make a GROMACS topology for a protein contained in a pdbįile. The rtp file extension stands for residue topology. xpm x - fontsize = 16 Font size ( pt ) x - font = Times - Roman A PostScript Font x - tickfontsize = 10 Font size ( pt ) x - tickfont = Helvetica A PostScript Font y - major = 20 y - minor = 5 y - firstmajor = 0 y - majorat0 = no y - majorticklen = 8.0 y - minorticklen = 4.0 y - label = y - fontsize = 16 y - font = Times - Roman y - tickfontsize = 10 y - tickfont = Helvetica Minor ticks x - firstmajor = 0 First frame for major tick x - majorat0 = no Major tick at first frame x - majorticklen = 8.0 x - majorticklength x - minorticklen = 4.0 x - minorticklength x - label = Used when there is none in the. xpm legend2label = Used when merging two xpm 's legendfontsize = 14 Font size ( pt ) xbox = 2.0 x - size of a matrix element ybox = 2.0 y - size of a matrix element matrixspacing = 20.0 Space between 2 matrices xoffset = 0.0 Between matrix and bounding box yoffset = 0.0 Between matrix and bounding box x - major = 20 Major ticks on x axis every. Command line options of xpm2ps override the parameters in this file black & white = no Obsolete titlefont = Times - Roman A PostScript Font titlefontsize = 20 Font size ( pt ) legend = yes Show the legend legendfont = Times - Roman A PostScript Font legendlabel = Used when there is none in the.