[gmx-users] Format for nonbonded interactions (pairs) in a residue definition

ashish bihani ashish.bihani at outlook.com
Thu Feb 26 02:49:47 CET 2015

PRODRG has generated force field parameters for Inositol Pyrophosphate (as mentioned in the tutorials). I reformatted atoms, bonds, bond angles, dihedrals and impropers by imitating the format followed in the definitions of other residues in aminoacids.rtp. But I am not able to find a format for [ pairs ].Unlike dihedrals, pairs defined in ffnonbonded file of gromos54A7 have not been assigned codes. If I have two columns for individual atoms (e.g. O35 tab P15 tab ?) involved in the interaction, how do I point the program to corresponding c6 and c12 values in ffnonbonded.itp? 		 	   		  

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