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Frosst_AlkEthOH_extracarbons.ffxml
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Frosst_AlkEthOH_extracarbons.ffxml
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<?xml version="1.0"?>
<SMIRNOFF version="1.0" aromaticity_model="OEAroModel_MDL">
<!-- SMIRNOFF (SMIRKS Native Open Force Field) mockup1.0 for alkanes, ethers, and alcohols -->
<Date>2016-09-02</Date>
<Author>C. I. Bayly, OpenEye Scientific Software and David Mobley, UCI</Author>
<!-- This mockup is based on frcmod.Frosst_AlkEthOH, the minimal subset of parm99/parm@Frosst -->
<!-- required for alkanes, ethers, and alcohols (excluding ketals and 3-memb-rings) -->
<!-- It has been extended to cover trivalent carbon in the same set, such as pentadiene and benzene, by adding additional bond, angle, and torsion parameters. Additionally, bond parameters for 6X3 were collapsed using partial bond orders. THIS IS NOT A COMPLETE FORCEFIELD AND IS PRESENT FOR TESTING PURPOSES.-->
<!-- WARNING: AMBER functional forms drop the factor of 2 in the bond energy term, so cross-comparing this file with a corresponding .frcmod file, it will appear that the values here are twice as large as they should be. -->
<Bonds potential="harmonic" length_unit="angstroms" k_unit="kilocalories_per_mole/angstrom**2" fractional_bondorder_method="Wiberg" fractional_bondorder_interpolation="linear">
<Bond smirks="[#6X4:1]-[#6X4:2]" length="1.526" k="620.0" id="b0001" parent_id="b0001"/> <!-- CT-CT from frcmod.Frosst_AlkEthOH -->
<Bond smirks="[#6X4:1]-[#1:2]" length="1.090" k="680.0" id="b0002" parent_id="b0002"/> <!-- CT-H_ from frcmod.Frosst_AlkEthOH -->
<Bond smirks="[#8:1]~[#1:2]" length="1.410" k="640.0" id="b0003" parent_id="b0003"/> <!-- DEBUG O-H -->
<Bond smirks="[#6X4:1]-[O&X2&H1:2]" length="1.410" k="640.0" id="b0004" parent_id="b0004"/> <!-- CT-OH from frcmod.Frosst_AlkEthOH -->
<Bond smirks="[#6X4:1]-[O&X2&H0:2]" length="1.370" k="640.0" id="b0005" parent_id="b0005"/> <!--CT-OS from frcmod.Frosst_AlkEthOH -->
<Bond smirks="[#8X2:1]-[#1:2]" length="0.960" k="1106.0" id="b0006" parent_id="b0003"/> <!-- OH-HO from frcmod.Frosst_AlkEthOH -->
<Bond smirks="[#6X3:1]!#[#6X3:2]" id="b5" k_bondorder1="820.0" k_bondorder2="1098" length_bondorder1="1.45" length_bondorder2="1.35"/> <!-- Christopher Bayly from parm99, Aug 2016 -->
<Bond smirks="[#6X3:1]-[#1:2]" id="b27" k="734.0" length="1.080"/> <!-- Christopher Bayly from parm99, Aug 2016 -->
</Bonds>
<!-- WARNING: AMBER functional forms drop the factor of 2 in the angle energy term, so cross-comparing this file with a corresponding .frcmod file, it will appear that the values here are twice as large as they should be. -->
<Angles angle_unit="degrees" k_unit="kilocalories_per_mole/radian**2">
<Angle smirks="[a,A:1]-[#6X4:2]-[a,A:3]" angle="109.50" k="100.0" id="a0001" parent_id="a0001"/> <!-- consensus matches all X-Csp3-X -->
<Angle smirks="[#1:1]-[#6X4:2]-[#1:3]" angle="109.50" k="70.0" id="a0002" parent_id="a0001"/> <!-- H1-CT-H1 from frcmod.Frosst_AlkEthOH -->
<Angle smirks="[#6X4:1]-[#6X4:2]-[#6X4:3]" angle="109.50" k="80.0" id="a0003" parent_id="a0001"/> <!-- CT-CT-CT from frcmod.Frosst_AlkEthOH -->
<Angle smirks="[#8X2:1]-[#6X4:2]-[#8X2:3]" angle="109.50" k="140.0" id="a0004" parent_id="a0001"/> <!-- O_-CT-O_ from frcmod.Frosst_AlkEthOH -->
<Angle smirks="[#6X4:1]-[#8X2:2]-[#1:3]" angle="108.50" k="110.0" id="a0005" parent_id="a0005"/> <!-- CT-OH-HO from frcmod.Frosst_AlkEthOH -->
<Angle smirks="[#6X4:1]-[#8X2:2]-[#6X4:3]" angle="109.50" k="120.0" id="a0006" parent_id="a0006"/> <!-- CT-OS-CT from frcmod.Frosst_AlkEthOH -->
<Angle smirks="[*:1]~[#6X3:2]~[*:3]" angle="120." id="a10" k="140.0"/> <!-- Christopher Bayly from parm99, Aug 2016 -->
<Angle smirks="[#1:1]-[#6X3:2]~[*:3]" angle="120." id="a11" k="100.0"/> <!-- Christopher Bayly from parm99, Aug 2016 -->
<Angle smirks="[#1:1]-[#6X3:2]-[#1:3]" angle="120." id="a12" k="70.0"/> <!-- Christopher Bayly from parm99, Aug 2016 -->
</Angles>
<ProperTorsions potential="charmm" phase_unit="degrees" k_unit="kilocalories_per_mole">
<Proper smirks="[a,A:1]-[#6X4:2]-[#6X4:3]-[a,A:4]" idivf1="9" periodicity1="3" phase1="0.0" k1="1.40" id="t0001" parent_id="t0001"/> <!-- X -CT-CT-X from frcmod.Frosst_AlkEthOH -->
<Proper smirks="[a,A:1]-[#6X4:2]-[#8X2:3]-[#1:4]" idivf1="3" periodicity1="3" phase1="0.0" k1="0.50" id="t0002" parent_id="t0002"/> <!--X -CT-OH-X from frcmod.Frosst_AlkEthOH -->
<Proper smirks="[a,A:1]-[#6X4:2]-[#8X2:3]-[!#1:4]" idivf1="3" periodicity1="3" phase1="0.0" k1="1.15" id="t0003" parent_id="t0003"/> <!-- X -CT-OS-X from frcmod.Frosst_AlkEthOH -->
<Proper smirks="[#1:1]-[#6X4:2]-[#6X4:3]-[#1:4]" idivf1="1" periodicity1="3" phase1="0.0" k1="0.15" id="t0004" parent_id="t0001"/> <!-- HC-CT-CT-HC from frcmod.Frosst_AlkEthOH; note discrepancy with parm@frosst which applies this ONLY to HC-CT-CT-HC and other hydrogens get the generic X -CT-CT-X -->
<Proper smirks="[#1:1]-[#6X4:2]-[#6X4:3]-[#6X4:4]" idivf1="1" periodicity1="3" phase1="0.0" k1="0.16" id="t0005" parent_id="t0001"/> <!-- HC-CT-CT-CT from frcmod.Frosst_AlkEthOH -->
<Proper smirks="[#6X4:1]-[#6X4:2]-[#8X2:3]-[#1:4]" idivf1='1' periodicity1="3" phase1="0.0" k1="0.16" idivf2="1" periodicity2="1" phase2="0.0" k2="0.25" id="t0006" parent_id="t0002"/> <!-- HO-OH-CT-CT from frcmod.Frosst_AlkEthOH -->
<Proper smirks="[#6X4:1]-[#6X4:2]-[#6X4:3]-[#6X4:4]" idivf1="1" periodicity1="3" phase1="0.0" k1="0.18" idivf2="1" periodicity2="2" phase2="180.0" k2="0.25" idivf3="1" periodicity3="1" phase3="180.0" k3="0.20" id="t0007" parent_id="t0001"/> <!-- CT-CT-CT-CT from frcmod.Frosst_AlkEthOH -->
<Proper smirks="[#6X4:1]-[#6X4:2]-[#8X2:3]-[#6X4:4]" idivf1="1" periodicity1="3" phase1="0.0" k1="0.383" idivf2="1" periodicity2="2" phase2="180.0" k2="0.1" id="t0008" parent_id="t0003"/> <!-- CT-CT-OS-CT from frcmod.Frosst_AlkEthOH -->
<Proper smirks="[#6X4:1]-[#8X2:2]-[#6X4:3]-[O&X2&H0:4]" idivf1="1" periodicity1="3" phase1="0.0" k1="0.10" idivf2="1" periodicity2="2" phase2="180.0" k2="0.85" idivf3="1" periodicity3="1" phase3="180.0" k3="1.35" id="t0009" parent_id="t0003"/> <!-- CT-OS-CT-OS from frcmod.Frosst_AlkEthOH -->
<Proper smirks="[#8X2:1]-[#6X4:2]-[#6X4:3]-[#8X2:4]" idivf1="1" periodicity1="3" phase1="0.0" k1="0.144" idivf2="1" periodicity2="2" phase2="0.0" k2="1.175" id="t0010" parent_id="t0001"/> <!-- O_-CT-CT-O_ from frcmod.Frosst_AlkEthOH -->
<Proper smirks="[#8X2:1]-[#6X4:2]-[#6X4:3]-[#1:4]" idivf1="1" periodicity1="3" phase1="0.0" k1="0.0" idivf2="1" periodicity2="1" phase2="0.0" k2="0.25" id="t0011" parent_id="t0001"/> <!-- H_-CT-CT-O_ from frcmod.Frosst_AlkEthOH; discrepancy with parm@frosst with H2,H3-CT-CT-O_ per C Bayly -->
<Proper smirks="[#1:1]-[#6X4:2]-[#6X4:3]-[OX2:4]" idivf1="1" periodicity1="3" phase1="0.0" k1="0.0" idivf2="1" periodicity2="1" phase2="0.0" k2="0.25" id="t0012" parent_id="t0001"/> <!-- HC,H1-CT-CT-OH,OS from frcmod.Frosst_AlkEthOH ; note corresponding H2 and H3 params missing so they presumably get generic parameters (another parm@frosst bug) -->
<Proper smirks="[*:1]~[#6X3:2]-[#6X4:3]~[*:4]" id="t13" idivf1="1" k1="0.000" periodicity1="3" phase1="0.0"/> <!-- parm99 generic, Bayly, Aug 2016 -->
<Proper smirks="[#1:1]-[#6X4:2]-[#6X3:3]=[#6X3:4]" id="t15" idivf1="1" k1="0.380" periodicity1="3" phase1="180.0" phase2="0.0" k2="1.150" periodicity2="1" idivf2="1"/> <!-- parm99, Bayly, Aug 2016 -->
<Proper smirks="[*:1]~[#6X3:2]-[#6X3:3]~[*:4]" id="t18" idivf1="1" k1="1." periodicity1="2" phase1="180.0"/> <!-- parm99 generic, Bayly, Aug 2016 -->
<Proper smirks="[*:1]~[#6X3:2]:[#6X3:3]~[*:4]" id="t20" idivf1="1" k1="3.625" periodicity1="2" phase1="180.0"/> <!-- parm99 generic, Bayly, Aug 2016 -->
<Proper smirks="[*:1]-[#6X3:2]=[#6X3:3]-[*:4]" id="t21" idivf1="1" k1="6." periodicity1="2" phase1="180.0"/> <!-- parm99 generic, Bayly, Aug 2016 -->
</ProperTorsions>
<ImproperTorsions potential="charmm" phase_unit="degrees" k_unit="kilocalories_per_mole">
<Improper smirks="[a,A:1]~[#6X3:2]([a,A:3])~[OX1:4]" periodicity1="2" phase1="180.0" k1="10.5" id="i0001" parent_id="i0001"/> <!-- X -X -C -O from frcmod.Frosst_AlkEthOH; none in set but here as format placeholder -->
</ImproperTorsions>
<!-- WARNING: AMBER formats typically use r_0/2=r_min/2 to describe the relevant distance parameter, where r0 = 2^(1/6)*sigma. The difference is important, and the two conventions can be used here by specifying sigma or rmin_half. -->
<vdW potential="Lennard-Jones-12-6" combining_rules="Loentz-Berthelot" scale12="0.0" scale13="0.0" scale14="0.5" scale15="1" sigma_unit="angstroms" epsilon_unit="kilocalories_per_mole" switch="8.0*angstroms" cutoff="9.0*angstroms" long_range_dispersion="isotropic">
<!-- sigma is in angstroms, epsilon is in kcal/mol -->
<Atom smirks="[#1:1]" rmin_half="1.4870" epsilon="0.0157" id="n0001" parent_id="n0001"/> <!-- making HC the generic hydrogen -->
<Atom smirks="[$([#1]-C):1]" rmin_half="1.4870" epsilon="0.0157" id="n0002" parent_id="n0001"/> <!-- HC from frcmod.Frosst_AlkEthOH -->
<Atom smirks="[$([#1]-C-[#7,#8,F,#16,Cl,Br]):1]" rmin_half="1.3870" epsilon="0.0157" id="n0003" parent_id="n0002"/> <!-- H1 from frcmod.Frosst_AlkEthOH -->
<Atom smirks="[$([#1]-C(-[#7,#8,F,#16,Cl,Br])-[#7,#8,F,#16,Cl,Br]):1]" rmin_half="1.2870" epsilon="0.0157" id="n0004" parent_id="n0003"/> <!--H2 from frcmod.Frosst_AlkEthOH -->
<Atom smirks="[$([#1]-C(-[#7,#8,F,#16,Cl,Br])(-[#7,#8,F,#16,Cl,Br])-[#7,#8,F,#16,Cl,Br]):1]" rmin_half="1.1870" epsilon="0.0157" id="n0005" parent_id="n0004"/> <!--H3 from frcmod.Frosst_AlkEthOH -->
<Atom smirks="[#1$(*-[#8]):1]" rmin_half="0.0000" epsilon="0.0000" id="n0006" parent_id="n0001"/> <!-- HO from frcmod.Frosst_AlkEthOH -->
<Atom smirks="[#6:1]" rmin_half="1.9080" epsilon="0.1094" id="n0007" parent_id="n0007"/> <!-- making CT the generic carbon -->
<Atom smirks="[#6X4:1]" rmin_half="1.9080" epsilon="0.1094" id="n0008" parent_id="n0007"/> <!-- CT from frcmod.Frosst_AlkEthOH-->
<Atom smirks="[#8:1]" rmin_half="1.6837" epsilon="0.1700" id="n0009" parent_id="n0009"/> <!-- making OS the generic oxygen -->
<Atom smirks="[#8X2:1]" rmin_half="1.6837" epsilon="0.1700" id="n0010" parent_id="n0009"/> <!-- OS from frcmod.Frosst_AlkEthOH -->
<Atom smirks="[#8X2+0$(*-[#1]):1]" rmin_half="1.7210" epsilon="0.2104" id="n0011" parent_id="n0009"/> <!-- OH from frcmod.Frosst_AlkEthOH -->
</vdW>
</SMIRNOFF>