-
Notifications
You must be signed in to change notification settings - Fork 8
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #44 from open-forcefield-group/smirff_energy_check
Finishing initial tests of SMIRFF against parm@frosst
- Loading branch information
Showing
2 changed files
with
72 additions
and
11 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| <?xml version="1.0"?> | ||
|
|
||
| <SMARFF> | ||
|
|
||
| <!-- SMARFF (SMARTS Force Field) mockup1.0 for alkanes, ethers, and alcohols --> | ||
| <Date>Date: Tue May 3 2016</Date> | ||
| <Author>C. I. Bayly, OpenEye Scientific Software</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) --> | ||
|
|
||
| <!-- 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. --> | ||
| <HarmonicBondForce length_unit="angstroms" k_unit="kilocalories_per_mole/angstrom**2"> | ||
| <Bond smirks="[#6X4:1]-[#6X4:2]" length="1.526" k="620.0"/> <!-- CT-CT from frcmod.Frosst_AlkEthOH --> | ||
| <Bond smirks="[#6X4:1]-[#1:2]" length="1.090" k="680.0"/> <!-- CT-H_ from frcmod.Frosst_AlkEthOH --> | ||
| <Bond smirks="[#8:1]~[#1:2]" length="1.410" k="640.0"/> <!-- DEBUG O-H --> | ||
| <Bond smirks="[#6X4:1]-[O&X2&H1:2]" length="1.410" k="640.0"/> <!-- CT-OH from frcmod.Frosst_AlkEthOH --> | ||
| <Bond smirks="[#6X4:1]-[O&X2&H0:2]" length="1.370" k="640.0"/> <!--CT-OS from frcmod.Frosst_AlkEthOH --> | ||
| <Bond smirks="[#8X2:1]-[#1:2]" length="0.960" k="1106.0"/> <!-- OH-HO from frcmod.Frosst_AlkEthOH --> | ||
| </HarmonicBondForce> | ||
| <!-- 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. --> | ||
| <HarmonicAngleForce 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"/> <!-- consensus matches all X-Csp3-X --> | ||
| <Angle smirks="[#1:1]-[#6X4:2]-[#1:3]" angle="109.50" k="70.0"/> <!-- H1-CT-H1 from frcmod.Frosst_AlkEthOH --> | ||
| <Angle smirks="[#6X4:1]-[#6X4:2]-[#6X4:3]" angle="109.50" k="80.0"/> <!-- CT-CT-CT from frcmod.Frosst_AlkEthOH --> | ||
| <Angle smirks="[#8X2:1]-[#6X4:2]-[#8X2:3]" angle="109.50" k="140.0"/> <!-- O_-CT-O_ from frcmod.Frosst_AlkEthOH --> | ||
| <Angle smirks="[#6X4:1]-[#8X2:2]-[#1:3]" angle="108.50" k="110.0"/> <!-- CT-OH-HO from frcmod.Frosst_AlkEthOH --> | ||
| <Angle smirks="[#6X4:1]-[#8X2:2]-[#6X4:3]" angle="109.50" k="120.0"/> <!-- CT-OS-CT from frcmod.Frosst_AlkEthOH --> | ||
| </HarmonicAngleForce> | ||
| <PeriodicTorsionForce 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"/> <!-- 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"/> <!--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"/> <!-- 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"/> <!-- HC-CT-CT-HC from frcmod.Frosst_AlkEthOH --> | ||
| <Proper smirks="[#1:1]-[#6X4:2]-[#6X4:3]-[#6X4:4]" idivf1="1" periodicity1="3" phase1="0.0" k1="0.16"/> <!-- HC-CT-CT-CT from frcmod.Frosst_AlkEthOH; note discrepancy from parm99/parm@frosst where this is applied to onlly HC-CT-CT-CT and not H1-CT-CT-CT, H2- or H3- torsions. --> | ||
| <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"/> <!-- 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"/> <!-- 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"/> <!-- CT-CT-OS-CT from frcmod.Frosst_AlkEthOH --> | ||
| <Proper smirks="[#6X4:1]-[#8X4:2]-[#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"/> <!-- 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"/> <!-- 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"/> <!-- 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](-[#8])-[#1:4]" idivf1="9" periodicity1="3" phase1="0.0" k1="1.40"/> <!-- X-CT-CT-X from parm99/parm@frosst applied to H1-CT-CT-H1, H2- and H3- torsions. This reproduces a parm99/parm@frosst bug where the generic X-CT-CT-X is erroneously applied to all H*-CT-CT-H* torsions EXCEPT HC-CT-CT-HC.. --> | ||
| <Proper smirks="[#1:1]-[#6X4:2](-[#8])-[#6X4:3]-[#6X4:4]" idivf1="9" periodicity1="3" phase1="0.0" k1="1.40"/> <!-- X -CT-CT-X from frcmod.Frosst_AlkEthOH applied to H1-CT-CT-CT, H2- and H3- torsions. This reproduces a parm99/parm@frosst bug where the generic X-CT-CT-X is erroneously applied to all H*-CT-CT-CT torsions EXCEPT HC-CT-CT-CT. --> | ||
| <Improper smirks="[a,A:1]~[#6X3:2]([a,A:3])~[OX1:4]" periodicity1="2" phase1="180.0" k1="10.5"/> <!-- X -X -C -O from frcmod.Frosst_AlkEthOH; none in set but here as format placeholder --> | ||
| </PeriodicTorsionForce> | ||
| <!-- 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. --> | ||
| <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5" sigma_unit="angstroms" epsilon_unit="kilocalories_per_mole"> | ||
| <!-- sigma is in angstroms, epsilon is in kcal/mol --> | ||
| <Atom smirks="[#1:1]" rmin_half="1.4870" epsilon="0.0157"/> <!-- making HC the generic hydrogen --> | ||
| <Atom smirks="[$([#1]-C):1]" rmin_half="1.4870" epsilon="0.0157"/> <!-- HC from frcmod.Frosst_AlkEthOH --> | ||
| <Atom smirks="[$([#1]-C-[#7,#8,F,#16,Cl,Br]):1]" rmin_half="1.3870" epsilon="0.0157"/> <!-- H1 from frcmod.Frosst_AlkEthOH --> | ||
| <Atom smirks="[$([#1]-C(-[#7,#8,F,#16,Cl,Br])-[#7,#8,F,#16,Cl,Br]):1]" rmin_half="1.2870" epsilon="0.0157"/> <!--H2 from frcmod.Frosst_AlkEthOH --> | ||
| <Atom smirks="[$([#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"/> <!--H3 from frcmod.Frosst_AlkEthOH --> | ||
| <Atom smirks="[#1$(*-[#8]):1]" rmin_half="0.0000" epsilon="0.0000"/> <!-- HO from frcmod.Frosst_AlkEthOH --> | ||
| <Atom smirks="[#6:1]" rmin_half="1.9080" epsilon="0.1094"/> <!-- making CT the generic carbon --> | ||
| <Atom smirks="[#6X4:1]" rmin_half="1.9080" epsilon="0.1094"/> <!-- CT from frcmod.Frosst_AlkEthOH--> | ||
| <Atom smirks="[#8:1]" rmin_half="1.6837" epsilon="0.1700"/> <!-- making OS the generic oxygen --> | ||
| <Atom smirks="[#8X2:1]" rmin_half="1.6837" epsilon="0.1700"/> <!-- OS from frcmod.Frosst_AlkEthOH --> | ||
| <Atom smirks="[#8X2+0$(*-[#1]):1]" rmin_half="1.7210" epsilon="0.2104"/> <!-- OH from frcmod.Frosst_AlkEthOH --> | ||
| </NonbondedForce> | ||
|
|
||
| </SMARFF> |