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Included DNA.OL24 forcefield #437

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b7fc626
Included AMBER's DNA.OL24 forcefield
Apr 12, 2026
da5b125
Fixed improper dihedrals in DNA.OL21.xml with epretti/parmed
Apr 12, 2026
dda096a
Converted OL21 and OL24 using https://github.com/epretti/ParmEd/commi…
Apr 25, 2026
e596caf
Deleted DNA.OL24.yaml
Apr 25, 2026
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12 changes: 12 additions & 0 deletions amber/DNA.OL24.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
- MODE: LEAPRC
- sourcePackage: AmberTools
sourcePackageVersion: "24.8"
- Source: ./files/DNA.OL24/leaprc.DNA.OL24
Prefix: DNA
Reference:
- >-
Zgarbova, M.; Sponer, J.; Jurecka, P,
Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field.
J. Chem. Theory Comput. 2025, https://doi.org/10.1021/acs.jctc.4c01100.
Test:
- dna
9 changes: 9 additions & 0 deletions amber/biopolymer.yaml
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Expand Up @@ -168,6 +168,15 @@
J. Chem. Theory Comput., 2021, 17, 6292-6301.
Test:
- dna
- Source: ./files/DNA.OL24/leaprc.DNA.OL24
Prefix: DNA
Reference:
- >-
Zgarbova, M.; Sponer, J.; Jurecka, P,
Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field.
J. Chem. Theory Comput. 2025, https://doi.org/10.1021/acs.jctc.4c01100.
Test:
- dna
- Source: leaprc.DNA.bsc1
Prefix: DNA
Reference:
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226 changes: 226 additions & 0 deletions amber/files/DNA.OL24/ff-nucleic-OL24.frcmod
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OL24 parameters for DNA, see http://ffol.upol.cz
MASS
C7 12.01 0.878 sp3 aliphatic C
C2 12.01 0.360 sp2 C 5 memb.ring in purines
C1 12.01 0.360 sp2 C pyrimidines in pos. 5 & 6
CJ 12.01

BOND
C7-CT 310.0 1.526 JCC,7,(1986),230; AA, SUGARS
C7-H1 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, RIBOSE
C7-OH 320.0 1.410 JCC,7,(1986),230; SUGARS
C7-OS 320.0 1.410 JCC,7,(1986),230; NUCLEIC ACJDS
C2-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE,GUA
C2-N* 440.0 1.371 JCC,7,(1986),230; ADE,GUA
C2-NB 529.0 1.304 JCC,7,(1986),230; ADE,GUA
C -C1 410.0 1.444 JCC,7,(1986),230; THY,URA
CA-C1 427.0 1.433 JCC,7,(1986),230; CYT
C1-C1 549.0 1.350 JCC,7,(1986),230; CYT,THY,URA
C1-CT 317.0 1.510 JCC,7,(1986),230; THY
C1-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA
C1-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA
C1-N* 448.0 1.365 JCC,7,(1986),230; CYT,THY,URA
CJ-H1 340.0 1.090
CJ-CT 310.0 1.526
OS-CJ 320.0 1.410
OH-CJ 320.0 1.410

ANGLE
H1-C7-OH 50.0 109.50 changed based on NMA nmodes
H1-C7-OS 50.0 109.50 changed based on NMA nmodes
C7-CT-CT 40.0 109.50
CT-C7-CT 40.0 109.50
C7-CT-HC 50.0 109.50 changed based on NMA nmodes
C7-CT-H1 50.0 109.50 changed based on NMA nmodes
CT-C7-H1 50.0 109.5
CT-C7-OH 50.0 109.50
CT-C7-OS 50.0 109.50
C7-CT-OS 50.0 109.50
C7-CT-OH 50.0 109.50
C7-OS-P 100.0 120.50
C7-OH-HO 55.0 108.50
CJ-CT-C7 40.0 109.50
H5-C2-N* 50.0 123.05
H5-C2-NB 50.0 123.05
N*-C2-NB 70.0 113.90
CB-N*-C2 70.0 105.40
C2-N*-CT 70.0 128.80
CB-NB-C2 70.0 103.80
C1-C -NA 70.0 114.10
C1-C -O 80.0 125.30
C1-CA-N2 70.0 120.10
C1-CA-NC 70.0 121.50
C -C1-C1 63.0 120.70 changed from 85.0 bsd on C6H6 nmodes; NA thy
C -C1-CT 70.0 119.70
C -C1-HA 50.0 119.70
C -C1-H4 50.0 119.70
CA-C1-C1 63.0 117.00 changed from 85.0 bsd on C6H6 nmodes; NA cyt
CA-C1-HA 50.0 123.30
CA-C1-H4 50.0 123.30
C1-C1-CT 70.0 119.70
C1-C1-HA 50.0 119.70
C1-C1-H4 50.0 119.70
C1-C1-N* 70.0 121.20
H4-C1-N* 50.0 119.10
H1-CT-C1 50.0 109.50 Junmei et al, 1999
HC-CT-C1 50.0 109.50 changed based on NMA nmodes
C -N*-C1 70.0 121.60
C1-N*-CT 70.0 121.20
H1-CJ-CT 50.0 109.50
H1-CJ-H1 35.0 109.50
CJ-CT-H1 50.0 109.50
CJ-CT-OS 50.0 109.50
CJ-CT-CT 40.0 109.50
OS-CJ-H1 50.0 109.50
OS-CJ-CT 50.0 109.50
P -OS-CJ 100.0 120.50
OH-CJ-H1 50.0 109.50
OH-CJ-CT 50.0 109.50
HO-OH-CJ 55.0 108.50

DIHEDRAL
CJ-OS-P-O2 3 0.75 0.0 3. to alpha
C7-OS-P-O2 1 0.29407 358.284 3. zet OL1
X -C7-OH-X 3 0.50 0.0 3. JCC,7,(1986),230
X -C7-OS-X 3 1.15 0.0 3. JCC,7,(1986),230
X -C7-CT-X 9 1.40 0.0 3. JCC,7,(1986),230
CT-C7-OS-P 1 0.15259 162.4967 -3. eps OL1
CT-C7-OS-P 1 0.64681 139.8342 -2. eps OL1
CT-C7-OS-P 1 1.77488 205.9192 1. eps OL1
OH-P -OS-C7 1 0.29407 358.284 -3. zet OL1
OH-P -OS-C7 1 0.97425 350.8820 -2. zet OL1
OH-P -OS-C7 1 0.92887 1.7533 1. zet OL1
OS-P -OS-C7 1 0.29407 358.284 -3. zet OL1
OS-P -OS-C7 1 0.97425 350.8820 -2. zet OL1
OS-P -OS-C7 1 0.92887 1.7533 1. zet OL1
HC-CT-C7-CT 1 0.16 0.0 3. Junmei et al, 1999
HO-OH-C7-CT 1 0.16 0.0 -3. Junmei et al, 1999
HO-OH-C7-CT 1 0.25 0.0 1. Junmei et al, 1999
CT-CT-C7-CT 1 0.18 0.0 -3. Junmei et al, 1999
CT-CT-C7-CT 1 0.25 180.0 -2. Junmei et al, 1999
CT-CT-C7-CT 1 0.20 180.0 1. Junmei et al, 1999
C7-CT-OS-CT 1 0.383 0.0 -3.
C7-CT-OS-CT 1 0.1 180.0 2.
OS-C7-CT-OS 1 0.144 0.0 -3. parm98, TC,PC,PAK
OS-C7-CT-OS 1 1.175 0.0 2. Piotr et al.
OS-C7-CT-OH 1 0.144 0.0 -3. parm98, TC,PC,PAK
OS-C7-CT-OH 1 1.175 0.0 2. Piotr et al.
OS-CT-C7-OH 1 0.144 0.0 -3. parm98, TC,PC,PAK
OS-CT-C7-OH 1 1.175 0.0 2. Piotr et al.
OH-CT-C7-OH 1 0.144 0.0 -3. parm98, TC,PC,PAK
OH-CT-C7-OH 1 1.175 0.0 2. Piotr et al.
H1-C7-CT-OS 1 0.000 0.0 -3. JCC,7,(1986),230
H1-C7-CT-OS 1 0.25 0.0 1. Junmei et al, 1999
H1-CT-C7-OS 1 0.000 0.0 -3. JCC,7,(1986),230
H1-CT-C7-OS 1 0.25 0.0 1. Junmei et al, 1999
H1-CT-C7-OH 1 0.000 0.0 -3. JCC,7,(1986),230
H1-CT-C7-OH 1 0.25 0.0 1. Junmei et al, 1999
H1-C7-CT-OH 1 0.000 0.0 -3. JCC,7,(1986),230
H1-C7-CT-OH 1 0.25 0.0 1. Junmei et al, 1999
HC-CT-C7-OS 1 0.000 0.0 -3. JCC,7,(1986),230
HC-CT-C7-OS 1 0.25 0.0 1. Junmei et al, 1999
HC-CT-C7-OH 1 0.000 0.0 -3. JCC,7,(1986),230
HC-CT-C7-OH 1 0.25 0.0 1. Junmei et al, 1999
CJ-CT-C7-CT 1 0.180 0.0 -3.0
CJ-CT-C7-CT 1 0.250 180.0 -2.0
CJ-CT-C7-CT 1 0.200 180.0 1.0
X -C2-N*-X 4 6.80 180.0 2. JCC,7,(1986),230
X -C2-NB-X 2 20.00 180.0 2. JCC,7,(1986),230
X -C -C1-X 4 8.70 180.0 2. intrpol.bsd.on C6H6
X -CA-C1-X 4 10.20 180.0 2. intrpol.bsd.on C6H6
X -C1-C1-X 4 26.60 180.0 2. intrpol.bsd.on C6H6
X -C1-CT-X 6 0.00 0.0 3. JCC,7,(1986),230
X -C1-N*-X 4 7.40 180.0 2. JCC,7,(1986),230
HC-CT-C1-C1 1 0.38 180.0 -3. Junmei et al, 1999
HC-CT-C1-C1 1 1.15 0.0 1. Junmei et al, 1999
C1-C1-C -O 1 2.175 180.0 -2. Junmei et al, 1999
C1-C1-C -O 1 0.30 0.0 3. Junmei et al, 1999
OS-CT-N*-C2 1 0.96561 68.7902 -1. ol3 chi ade
OS-CT-N*-C2 1 1.07403 15.6360 -2. ol3 chi ade
OS-CT-N*-C2 1 0.45754 171.5787 -3. ol3 chi ade
OS-CT-N*-C2 1 0.30917 19.0921 4. ol3 chi ade
OS-CT-N*-CK 1 0.70510 74.7558 -1. ol3 chi gua
OS-CT-N*-CK 1 1.06546 6.2286 -2. ol3 chi gua
OS-CT-N*-CK 1 0.44273 168.6503 -3. ol3 chi gua
OS-CT-N*-CK 1 0.25602 3.9746 4. ol3 chi gua
OS-CT-N*-C1 1 1.22506 146.9892 -1. ol3 chi cyt
OS-CT-N*-C1 1 1.63459 16.4766 -2. ol3 chi cyt
OS-CT-N*-C1 1 0.93747 185.8774 -3. ol3 chi cyt
OS-CT-N*-C1 1 0.31033 32.1590 4. ol3 chi cyt
OS-CT-N*-CM 1 1.02514 149.8583 -1. ol3 chi ura,thy
OS-CT-N*-CM 1 1.74876 16.7648 -2. ol3 chi ura,thy
OS-CT-N*-CM 1 0.58150 179.3474 -3. ol3 chi ura,thy
OS-CT-N*-CM 1 0.35148 16.0016 4. ol3 chi ura,thy
X -CJ-OS-X 3 1.150 0.0 3.0
X -CJ-OH-X 3 0.500 0.0 3.0
X -CJ-CT-X 9 1.400 0.0 3.0
CT-OS-CT-CJ 1 0.383 0.0 -3.0
CT-OS-CT-CJ 1 0.100 180.0 2.0
H1-CJ-CT-OS 1 0.250 0.0 1.0
H1-CJ-CT-OH 1 0.250 0.0 1.0
H1-CT-CJ-OS 1 0.250 0.0 1.0
H1-CT-CJ-OH 1 0.250 0.0 1.0
CJ-CT-CT-CT 1 0.180 0.0 -3.0
CJ-CT-CT-CT 1 0.250 180.0 -2.0
CJ-CT-CT-CT 1 0.200 180.0 1.0
OS-P -OS-CJ 1 0.316418 102.064 -1.0 alpha OL21
OS-P -OS-CJ 1 0.630096 359.693 -2.0 alpha OL21
OS-P -OS-CJ 1 0.241150 299.870 -3.0 alpha OL21
OS-P -OS-CJ 1 0.162591 32.081 -4.0 alpha OL21
OS-P -OS-CJ 1 0.097520 303.556 -5.0 alpha OL21
OS-P -OS-CJ 1 0.043252 19.494 6.0 alpha OL21
OH-P -OS-CJ 1 0.316418 102.064 -1.0 alpha OL21
OH-P -OS-CJ 1 0.630096 359.693 -2.0 alpha OL21
OH-P -OS-CJ 1 0.241150 299.870 -3.0 alpha OL21
OH-P -OS-CJ 1 0.162591 32.081 -4.0 alpha OL21
OH-P -OS-CJ 1 0.097520 303.556 -5.0 alpha OL21
OH-P -OS-CJ 1 0.043252 19.494 6.0 alpha OL21
C7-CT-CJ-OS 1 0.44673 166.468 -1.0 gamma OL21
C7-CT-CJ-OS 1 0.38415 245.817 -2.0 gamma OL21
C7-CT-CJ-OS 1 0.75142 343.954 -3.0 gamma OL21
C7-CT-CJ-OS 1 0.13943 276.030 -4.0 gamma OL21
C7-CT-CJ-OS 1 0.04362 305.263 -5.0 gamma OL21
C7-CT-CJ-OS 1 0.03838 141.188 6.0 gamma OL21
C7-CT-CJ-OH 1 0.44673 166.468 -1.0 gamma OL21
C7-CT-CJ-OH 1 0.38415 245.817 -2.0 gamma OL21
C7-CT-CJ-OH 1 0.75142 343.954 -3.0 gamma OL21
C7-CT-CJ-OH 1 0.13943 276.030 -4.0 gamma OL21
C7-CT-CJ-OH 1 0.04362 305.263 -5.0 gamma OL21
C7-CT-CJ-OH 1 0.03838 141.188 6.0 gamma OL21
CT-CJ-OS-P 1 0.527950 23.57816 -1.0 beta OL1
CT-CJ-OS-P 1 0.091274 223.64797 -2.0 beta OL1
CT-CJ-OS-P 1 0.535535 181.60702 -3.0 beta OL1
CT-CJ-OS-P 1 0.079760 215.18103 4.0 beta OL1
OS-C7-CT-CJ 1 0.023759 175.82681 -1.0 delta OL24
OS-C7-CT-CJ 1 4.412690 86.82802 -2.0 delta OL24
OS-C7-CT-CJ 1 6.539088 32.48510 -3.0 delta OL24
OS-C7-CT-CJ 1 4.131931 1.23464 -4.0 delta OL24
OS-C7-CT-CJ 1 1.715521 352.75760 -5.0 delta OL24
OS-C7-CT-CJ 1 0.800720 0.90184 6.0 delta OL24
OH-C7-CT-CJ 1 0.023759 175.82681 -1.0 delta OL24
OH-C7-CT-CJ 1 4.412690 86.82802 -2.0 delta OL24
OH-C7-CT-CJ 1 6.539088 32.48510 -3.0 delta OL24
OH-C7-CT-CJ 1 4.131931 1.23464 -4.0 delta OL24
OH-C7-CT-CJ 1 1.715521 352.75760 -5.0 delta OL24
OH-C7-CT-CJ 1 0.800720 0.90184 6.0 delta OL24
OS-CT-CT-C7 1 2.408206 129.97264 -1.0 tau1 OL24
OS-CT-CT-C7 1 6.999992 192.50081 -2.0 tau1 OL24
OS-CT-CT-C7 1 0.005635 58.18394 -3.0 tau1 OL24
OS-CT-CT-C7 1 3.342656 320.25110 -4.0 tau1 OL24
OS-CT-CT-C7 1 6.965447 74.12410 -5.0 tau1 OL24
OS-CT-CT-C7 1 4.111119 250.30732 6.0 tau1 OL24

IMPROPER
X -X -C2-H5 1.1 180. 2.
CB-C2-N*-CT 1.0 180. 2.
X -X -C1-H4 1.1 180. 2.
X -X -C1-HA 1.1 180. 2.
C -C1-N*-CT 1.0 180. 2. dac guess, 9/94
C -C1-C1-CT 1.1 180. 2. dac guess, 9/94
C1-N2-CA-NC 1.1 180. 2. dac guess, 9/94

NONBOND
C7 1.9080 0.1094 Spellmeyer
C2 1.9080 0.0860 Spellmeyer
C1 1.9080 0.0860 Spellmeyer
CJ 1.9080 0.1094
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