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eprettiepretti
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Add regenerated force fields that have fixes
1 parent c3a7103 commit d1cf1e2

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4 files changed

+49
-37
lines changed

4 files changed

+49
-37
lines changed

‎openmmforcefields/ffxml/amber/ff03.xml‎

Lines changed: 3 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
<ForceField>
22
<Info>
3-
<DateGenerated>2025-04-30</DateGenerated>
3+
<DateGenerated>2025-09-05</DateGenerated>
44
<Source Source="oldff/leaprc.ff03" md5hash="1b02b527c96d2a5f064a3f8465a4a9a2" sourcePackage="AmberTools" sourcePackageVersion="24.8">oldff/leaprc.ff03</Source>
55
<Reference>Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., et al. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24, 1999-2012.</Reference>
66
<Reference>Lee, M.C., and Duan, Y. (2004). Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins 55, 620-634.</Reference>
@@ -3058,8 +3058,7 @@
30583058
<Bond atomName1="CH3" atomName2="HH32"/>
30593059
<Bond atomName1="CH3" atomName2="HH33"/>
30603060
<ExternalBond atomName="N"/>
3061-
<ExternalBond atomName="CH3"/>
3062-
</Residue>
3061+
</Residue>
30633062
<Residue name="ACE">
30643063
<Atom name="HH31" type="HC" charge="0.07601"/>
30653064
<Atom name="CH3" type="CT" charge="-0.190263"/>
@@ -3072,7 +3071,6 @@
30723071
<Bond atomName1="CH3" atomName2="HH33"/>
30733072
<Bond atomName1="CH3" atomName2="C"/>
30743073
<Bond atomName1="C" atomName2="O"/>
3075-
<ExternalBond atomName="HH31"/>
30763074
<ExternalBond atomName="C"/>
30773075
</Residue>
30783076
<Residue name="NALA">
@@ -5387,4 +5385,4 @@
53875385
<Atom class="SH" sigma="0.35635948725613575" epsilon="1.046"/>
53885386
<Atom class="H0" sigma="0.2471353044121301" epsilon="0.06568879999999999"/>
53895387
</NonbondedForce>
5390-
</ForceField>
5388+
</ForceField>

‎openmmforcefields/ffxml/amber/ff14SB.xml‎

Lines changed: 24 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
<ForceField>
22
<Info>
3-
<DateGenerated>2025-04-30</DateGenerated>
3+
<DateGenerated>2025-09-05</DateGenerated>
44
<Source Source="oldff/leaprc.ff14SB" md5hash="7f016ac76ca64b68cb03725d6d370de8" sourcePackage="AmberTools" sourcePackageVersion="24.8">oldff/leaprc.ff14SB</Source>
55
<Reference>Maier, J.A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K.E., and Simmerling, C. (2015). ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. J. Chem. Theory Comput. 11, 3696-3713.</Reference>
66
</Info>
@@ -45,6 +45,7 @@
4545
<Type element="O" name="O2" class="O2" mass="16.0"/>
4646
<Type element="O" name="OH" class="OH" mass="16.0"/>
4747
<Type element="O" name="OS" class="OS" mass="16.0"/>
48+
<Type element="O" name="OP" class="OP" mass="16.0"/>
4849
<Type element="P" name="P" class="P" mass="30.97"/>
4950
<Type element="S" name="S" class="S" mass="32.06"/>
5051
<Type element="S" name="SH" class="SH" mass="32.06"/>
@@ -5082,6 +5083,7 @@
50825083
<Bond class1="CV" class2="NB" length="0.1394" k="343087.99999999994"/>
50835084
<Bond class1="CW" class2="H4" length="0.10800000000000001" k="307105.5999999999"/>
50845085
<Bond class1="CW" class2="NA" length="0.1381" k="357313.5999999999"/>
5086+
<Bond class1="OP" class2="P" length="0.148" k="439319.99999999994"/>
50855087
<Bond class1="O2" class2="P" length="0.148" k="439319.99999999994"/>
50865088
<Bond class1="OH" class2="P" length="0.16100000000000003" k="192463.99999999997"/>
50875089
<Bond class1="OS" class2="P" length="0.16100000000000003" k="192463.99999999997"/>
@@ -5153,6 +5155,7 @@
51535155
<Angle class1="CA" class2="C" class3="OS" angle="2.0943951023931953" k="585.76"/>
51545156
<Angle class1="CC" class2="NA" class3="P" angle="2.1834068942449063" k="641.8256"/>
51555157
<Angle class1="CR" class2="NA" class3="P" angle="2.1834068942449063" k="641.8256"/>
5158+
<Angle class1="NA" class2="P" class3="OP" angle="1.7868680881917944" k="358.98720000000003"/>
51565159
<Angle class1="CB" class2="C" class3="NA" angle="1.9425514574696887" k="585.76"/>
51575160
<Angle class1="CB" class2="C" class3="O" angle="2.2479840765686965" k="669.44"/>
51585161
<Angle class1="CM" class2="C" class3="NA" angle="1.99142067652553" k="585.76"/>
@@ -5425,6 +5428,8 @@
54255428
<Angle class1="P" class2="OS" class3="P" angle="2.1031217486531673" k="836.8000000000001"/>
54265429
<Angle class1="O2" class2="P" class3="OH" angle="1.888969849433463" k="376.56"/>
54275430
<Angle class1="O2" class2="P" class3="O2" angle="2.092649773141201" k="1171.52"/>
5431+
<Angle class1="OP" class2="P" class3="OP" angle="2.092649773141201" k="1171.52"/>
5432+
<Angle class1="OP" class2="P" class3="OS" angle="1.888969849433463" k="836.8000000000001"/>
54285433
<Angle class1="O2" class2="P" class3="OS" angle="1.888969849433463" k="836.8000000000001"/>
54295434
<Angle class1="OH" class2="P" class3="OS" angle="1.790707812546182" k="376.56"/>
54305435
<Angle class1="OS" class2="P" class3="OS" angle="1.790707812546182" k="376.56"/>
@@ -5678,6 +5683,9 @@
56785683
<Proper class1="H1" class2="CT" class3="CI" class4="OS" periodicity1="3" phase1="0.0" k1="0.0" periodicity2="1" phase2="0.0" k2="1.046"/>
56795684
<Proper class1="H1" class2="CT" class3="CI" class4="OH" periodicity1="3" phase1="0.0" k1="0.0" periodicity2="1" phase2="0.0" k2="1.046"/>
56805685
<Proper class1="CI" class2="CT" class3="CT" class4="CT" periodicity1="3" phase1="0.0" k1="0.75312" periodicity2="2" phase2="3.141592653589793" k2="1.046" periodicity3="1" phase3="3.141592653589793" k3="0.8368000000000001"/>
5686+
<Proper class1="OP" class2="P" class3="OS" class4="CA" periodicity1="3" phase1="3.141592653589793" k1="0.0" periodicity2="1" phase2="3.141592653589793" k2="0.0"/>
5687+
<Proper class1="CC" class2="NA" class3="P" class4="OP" periodicity1="3" phase1="0.0" k1="1.00416"/>
5688+
<Proper class1="CR" class2="NA" class3="P" class4="OP" periodicity1="3" phase1="0.0" k1="0.0"/>
56815689
<Proper class1="OS" class2="P" class3="OS" class4="CI" periodicity1="1" phase1="0.5549288319349986" k1="0.7747973040000001" periodicity2="2" phase2="6.142853854002235" k2="5.257325704" periodicity3="3" phase3="6.235144770452592" k3="1.484725872"/>
56825690
<Proper class1="OH" class2="P" class3="OS" class4="CI" periodicity1="1" phase1="0.5549288319349986" k1="0.7747973040000001" periodicity2="2" phase2="6.142853854002235" k2="5.257325704" periodicity3="3" phase3="6.235144770452592" k3="1.484725872"/>
56835691
<Proper class1="CT" class2="CT" class3="CI" class4="OS" periodicity1="1" phase1="3.3331692425337263" k1="4.92891936" periodicity2="2" phase2="5.159765562356967" k2="0.385354768" periodicity3="3" phase3="6.0754099683820435" k3="4.02848072"/>
@@ -5890,7 +5898,7 @@
58905898
<Improper class1="NA" class2="" class3="" class4="H" periodicity1="2" phase1="3.141592653589793" k1="4.184"/>
58915899
<Improper class1="CA" class2="" class3="N2" class4="N2" periodicity1="2" phase1="3.141592653589793" k1="43.932"/>
58925900
<Improper class1="N" class2="" class3="CT" class4="CT" periodicity1="2" phase1="3.141592653589793" k1="4.184"/>
5893-
<Improper class1="N" class2="" class3="CX" class4="CT" periodicity1="2" phase1="3.141592653589793" k1="4.184"/>
5901+
<Improper class1="N" class2="" class3="CT" class4="CX" periodicity1="2" phase1="3.141592653589793" k1="4.184"/>
58945902
<Improper class1="CA" class2="" class3="" class4="HA" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
58955903
<Improper class1="CW" class2="" class3="" class4="H4" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
58965904
<Improper class1="CR" class2="" class3="" class4="H5" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
@@ -5933,27 +5941,27 @@
59335941
<Improper class1="N" class2="C" class3="CX" class4="H" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
59345942
<Improper class1="N" class2="C" class3="CT" class4="O" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
59355943
<Improper class1="C5" class2="" class3="" class4="H5" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
5936-
<Improper class1="N*" class2="C5" class3="CB" class4="CT" periodicity1="2" phase1="3.141592653589793" k1="4.184"/>
5944+
<Improper class1="N*" class2="CB" class3="C5" class4="CT" periodicity1="2" phase1="3.141592653589793" k1="4.184"/>
59375945
<Improper class1="C4" class2="" class3="" class4="H4" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
59385946
<Improper class1="C4" class2="" class3="" class4="HA" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
59395947
<Improper class1="N*" class2="C" class3="C4" class4="CT" periodicity1="2" phase1="3.141592653589793" k1="4.184"/>
59405948
<Improper class1="C4" class2="C" class3="C4" class4="CT" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
59415949
<Improper class1="CA" class2="C4" class3="N2" class4="NC" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
59425950
<Improper class1="C" class2="CA" class3="CA" class4="OS" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
5943-
<Improper class1="NA" class2="CC" class3="CR" class4="P" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
5944-
<Improper class1="CB" class2="C*" class3="CA" class4="CN" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5945-
<Improper class1="CN" class2="CA" class3="CB" class4="NA" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5946-
<Improper class1="CB" class2="CB" class3="N*" class4="NC" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5947-
<Improper class1="CB" class2="C" class3="CB" class4="NB" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5948-
<Improper class1="CB" class2="CA" class3="CB" class4="NB" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5949-
<Improper class1="CJ" class2="H1" class3="H1" class4="OH" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5950-
<Improper class1="CJ" class2="CT" class3="H1" class4="OH" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5951-
<Improper class1="CJ" class2="CT" class3="H1" class4="H1" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5952-
<Improper class1="CJ" class2="H1" class3="H1" class4="OS" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5953-
<Improper class1="CJ" class2="CT" class3="H1" class4="OS" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5951+
<Improper class1="NA" class2="CR" class3="CC" class4="P" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
5952+
<Improper class1="CB" class2="C*" class3="CN" class4="CA" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5953+
<Improper class1="CN" class2="NA" class3="CA" class4="CB" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5954+
<Improper class1="CB" class2="N*" class3="CB" class4="NC" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5955+
<Improper class1="CB" class2="NB" class3="C" class4="CB" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5956+
<Improper class1="CB" class2="NB" class3="CA" class4="CB" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5957+
<Improper class1="CJ" class2="OH" class3="H1" class4="H1" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5958+
<Improper class1="CJ" class2="OH" class3="H1" class4="CT" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5959+
<Improper class1="CJ" class2="H1" class3="H1" class4="CT" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5960+
<Improper class1="CJ" class2="OS" class3="H1" class4="H1" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
5961+
<Improper class1="CJ" class2="OS" class3="H1" class4="CT" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
59545962
<Improper class1="CO" class2="" class3="O2" class4="O2" periodicity1="2" phase1="3.141592653589793" k1="43.932"/>
59555963
<Improper class1="C" class2="2C" class3="O" class4="OH" periodicity1="2" phase1="3.141592653589793" k1="43.932"/>
5956-
<Improper class1="CA" class2="2C" class3="CA" class4="CA" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
5964+
<Improper class1="CA" class2="CA" class3="CA" class4="2C" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
59575965
</PeriodicTorsionForce>
59585966
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
59595967
<UseAttributeFromResidue name="charge"/>
@@ -5997,6 +6005,7 @@
59976005
<Atom class="O2" sigma="0.2959921901149463" epsilon="0.87864"/>
59986006
<Atom class="OH" sigma="0.3066473387839048" epsilon="0.8803136"/>
59996007
<Atom class="OS" sigma="0.3000012343465779" epsilon="0.7112800000000001"/>
6008+
<Atom class="OP" sigma="0.3296325257119256" epsilon="0.7112800000000001"/>
60006009
<Atom class="P" sigma="0.37417746161894255" epsilon="0.8368000000000001"/>
60016010
<Atom class="S" sigma="0.35635948725613575" epsilon="1.046"/>
60026011
<Atom class="SH" sigma="0.35635948725613575" epsilon="1.046"/>

‎openmmforcefields/ffxml/amber/protein.ff03.r1.xml‎

Lines changed: 3 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
<ForceField>
22
<Info>
3-
<DateGenerated>2025-04-30</DateGenerated>
3+
<DateGenerated>2025-09-05</DateGenerated>
44
<Source Source="leaprc.protein.ff03.r1" md5hash="0bc4d048031a1f64ea910a6266ba6b51" sourcePackage="AmberTools" sourcePackageVersion="24.8">leaprc.protein.ff03.r1</Source>
55
<Reference>Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., et al. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24, 1999-2012.</Reference>
66
<Reference>Lee, M.C., and Duan, Y. (2004). Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins 55, 620-634.</Reference>
@@ -873,8 +873,7 @@
873873
<Bond atomName1="CH3" atomName2="HH32"/>
874874
<Bond atomName1="CH3" atomName2="HH33"/>
875875
<ExternalBond atomName="N"/>
876-
<ExternalBond atomName="CH3"/>
877-
</Residue>
876+
</Residue>
878877
<Residue name="ACE">
879878
<Atom name="HH31" type="protein-HC" charge="0.07601"/>
880879
<Atom name="CH3" type="protein-CT" charge="-0.190263"/>
@@ -887,7 +886,6 @@
887886
<Bond atomName1="CH3" atomName2="HH33"/>
888887
<Bond atomName1="CH3" atomName2="C"/>
889888
<Bond atomName1="C" atomName2="O"/>
890-
<ExternalBond atomName="HH31"/>
891889
<ExternalBond atomName="C"/>
892890
</Residue>
893891
<Residue name="NALA">
@@ -3011,4 +3009,4 @@
30113009
<Atom class="protein-SH" sigma="0.35635948725613575" epsilon="1.046"/>
30123010
<Atom class="protein-H0" sigma="0.2471353044121301" epsilon="0.06568879999999999"/>
30133011
</NonbondedForce>
3014-
</ForceField>
3012+
</ForceField>

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