rtp file format
|Main Table of Contents||VERSION 5.0.7|
gmx pdb2gmx automatically generates all angles, this means that the [angles] field is only useful for overriding .itp parameters.
gmx pdb2gmx automatically generates one proper dihedral for every rotatable bond, preferably on heavy atoms. When the [dihedrals] field is used, no other dihedrals will be generated for the bonds corresponding to the specified dihedrals. It is possible to put more than one dihedral on a rotatable bond.
gmx pdb2gmx sets the number exclusions to 3, which means that interactions between atoms connected by at most 3 bonds are excluded. Pair interactions are generated for all pairs of atoms which are seperated by 3 bonds (except pairs of hydrogens). When more interactions need to be excluded, or some pair interactions should not be generated, an [exclusions] field can be added, followed by pairs of atom names on seperate lines. All non-bonded and pair interactions between these atoms will be excluded.
A sample is included below.
[ bondedtypes ] ; mandatory ; bonds angles dihedrals impropers 1 1 1 2 ; mandatory [ GLY ] ; mandatory [ atoms ] ; mandatory ; name type charge chargegroup N N -0.280 0 H H 0.280 0 CA CH2 0.000 1 C C 0.380 2 O O -0.380 2 [ bonds ] ; optional ;atom1 atom2 b0 kb N H N CA CA C C O -C N [ exclusions ] ; optional ;atom1 atom2 [ angles ] ; optional ;atom1 atom2 atom3 th0 cth [ dihedrals ] ; optional ;atom1 atom2 atom3 atom4 phi0 cp mult [ impropers ] ; optional ;atom1 atom2 atom3 atom4 q0 cq N -C CA H -C -CA N -O [ ZN ] [ atoms ] ZN ZN 2.000 0