You should get the tleap message Using ArgH and AspGluO modified Bondi2 radiiĤ. For a thorough discussion of the theory and different parameters, see Cramer and Truhlar. Implicit solvent calculations use an electric field to mimic the solvent and the Generalized Born model is a common implimentation.
Use GBneck2 radii for implicit solvent calculation. Loading library: /amber20/dat/leap/lib/aminont12.libģ. Loading library: /amber20/dat/leap/lib/aminoct12.lib Loading library: /amber20/dat/leap/lib/amino12.lib Loading parameters: /amber20/dat/leap/parm/frcmod.ff99SB14įf99SB backbone parameters (Hornak & Simmerling) with ff14SB atom types Reading force field modification type file (frcmod)įf14SB protein backbone and sidechain parameters Loading parameters: /amber20/dat/leap/parm/frcmod.ff14SB PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + O元 for RNA Loading parameters: /amber20/dat/leap/parm/parm10.dat Source of /amber20/dat/leap/cmd/14SBonlysc done Source: /amber20/dat/leap/cmd/14SBonlysc
This tutorial uses the 10 amino acid peptide chignolin. Note that if you want to run implicit solvent simulations, you will want to specify your radii before saving your topology and input coordinate files.
ACID PRO 4 TUTORIAL HOW TO
This short tutorial shows you how to build a sequence, choose the correct force field and save an inputs for sander or pmemd. If you want to start a simulation from an extended structure and not based upon an experimentally-determined structure, then the sequence command in LEaP will make this starting structure for you.