def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None): custom = CustomGBForce() custom.addPerParticleParameter("q"); custom.addPerParticleParameter("radius"); custom.addPerParticleParameter("scale"); custom.addGlobalParameter("solventDielectric", solventDielectric); custom.addGlobalParameter("soluteDielectric", soluteDielectric); custom.addGlobalParameter("offset", 0.009) custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" "U=r+sr2;" "L=max(or1, D);" "D=abs(r-sr2);" "sr2 = scale2*or2;" "or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions) custom.addComputedValue("B", "1/(1/or-tanh(psi-0.8*psi^2+4.85*psi^3)/radius);" "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle) custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle) if SA=='ACE': custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle) elif SA is not None: raise ValueError('Unknown surface area method: '+SA) custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;" "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions) return custom
def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None): """ Indexing for tables: input: radius1, radius2 index = (radius2*200-20)*21 + (radius1*200-20) output: index of desired value in row-by-row, 1D version of Tables 3 & 4 """ custom = CustomGBForce() custom.addPerParticleParameter("q"); custom.addPerParticleParameter("radius"); custom.addPerParticleParameter("scale"); custom.addGlobalParameter("solventDielectric", solventDielectric); custom.addGlobalParameter("soluteDielectric", soluteDielectric); custom.addGlobalParameter("offset", 0.009) custom.addGlobalParameter("neckScale", 0.361825) custom.addGlobalParameter("neckCut", 0.68) custom.addFunction("getd0", d0, 0, 440) custom.addFunction("getm0", m0, 0, 440) custom.addComputedValue("I", "Ivdw+neckScale*Ineck;" "Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);" "index = (radius2*200-20)*21 + (radius1*200-20);" "Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" "U=r+sr2;" "L=max(or1, D);" "D=abs(r-sr2);" "sr2 = scale2*or2;" "or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions) custom.addComputedValue("B", "1/(1/or-tanh(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);" "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle) custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle) if SA=='ACE': custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle) elif SA is not None: raise ValueError('Unknown surface area method: '+SA) custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;" "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions) return custom