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This is the summary of our implementation of the AMBER99SB-UCB force field for GROMACS.
https://doi.org/10.1021/ct2000183 https://doi.org/10.1021/jp2118373
are the two reference papers for this force field. Please cite them when you are using our implementation.
This particular implementation is done by
Mohammed Khaled, Batuhan Kav, and Birgit Strodel at the Forschungszentrum Juelich, Germany.
For all inquiries, problems, and error reports, please contact b.strodel [at] fz-juelich.de
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First: add the new atoms HQ,NQ,and OR
edit aminoacids.rtp 1)add HQ (primery amide) for ASN, GLN, and LYN(neutral LYS)
ASN HD21 H change to HD21 HQ HD22 H change to HD22 HQ NASN HD21 H change to HD21 HQ HD22 H change to HD22 HQ CASN HD21 H change to HD21 HQ HD22 H change to HD22 HQ
GLN HE21 H change to HE21 HQ HE22 H change to HE22 HQ NGLN HE21 H change to HE21 HQ HE22 H change to HE22 HQ CGLN HE21 H change to HE21 HQ HE22 H change to HE22 HQ
LYN (neutral LYS) HZ1 H change to HZ1 HQ HZ2 H change to HZ2 HQ
2)add NQ (ASN, GLN and neutral LYS) #DONE!
ASN ND2 N change to ND2 NQ NASN ND2 N change to ND2 NQ CASN ND2 N change to ND2 NQ
GLN NE2 N change to NE2 NQ NGLN NE2 N change to NE2 NQ CGLN NE2 N change to NE2 NQ
LYN (neutral LYS) NZ N change to NZ NQ
- add OR (phenols(TYR)) #DONE!
TYR OH OH change to OH OR CTYR OH OH change to OH OR NTYR OH OH change to OH OR
######################################################################### edit atomtype.atp #DONE! add: HQ 1.00800 ; new amber99sb-ucb,ASN,GLN,LYN(neutral LYS) NQ 14.01000 ; new amber99sb-ucb,ASN,GLN,LYN(neutral LYS) OR 16.00000 ; new amber99sb-ucb,TYR
######################################################################### edit ffbonded.itp
First: edit phi dihedral angle potenatil term n=2: 8.36800 change to 7.53120
CT CT N C 9 0.0 7.53120 2 ; new amber99sb-ucb(8.36800 for amber99sb)
Second:We need to define the new bonds,angles,proper dihederals and impropers dihederals for ASN, GLN, LYN and TYR from aminoacids.rtp and then add them to ffbonded.itp
######### New bonds ############## 1)ASN CG ND2: define new bond C NQ ,same bonded parameters as C N bond ND2 HD21 and ND2 HD22: define new bond NQ HQ ,same bonded parameters as N H bond
2)GlN CD NE2:define new C NQ, same bonded parameters as C N NE2 HE21 and NE2 HE22: define new bond NQ HQ,same bonded parameters as N H
3)LYN CE NZ: define new bond CT NQ, same bonded parameters as CT N3 NZ HZ1 and NZ HZ2: define new bond NQ HQ, same bonded parameters as N H
4)TYR CZ OH change to C OR, same bonded parameters as C OH bond OH HH change to OR HO,same bonded parameters as OH HO bond
add new bonds to ffbonded.itp: #DONE!
C OR 1 0.13640 376560.0 ; new amber99sb-ucb,TYR HO OR 1 0.09600 462750.4 ; new amber99sb-ucb,TYR C NQ 1 0.13350 410032.0 ; new amber99sb-ucb,ASN,GLN CT NQ 1 0.14710 307105.6 ; new amber99sb-ucb,LYN(neutral LYS) HQ NQ 1 0.10100 363171.2 ; new amber99sb-ucb,ASN,GLN,LYN(neutral LYS)
######### New Angles ############## new angles:
- ASN and GLN C NQ HQ 1 120.000 418.400 ; new amber99sb-ucb,ASN,GLN /same angle parameters as: C N H 1 120.000 418.400 ; new99 general, gln, asn,changed based on NMA nmodes HQ NQ HQ 1 120.000 292.880 ; new amber99sb-ucb,ASN,GLN /same angle parameters as: H N H 1 120.000 292.880 ;ade,cyt,gua,gln,asn CT C NQ 1 116.600 585.760 ; new amber99sb-ucb,ASN,GLN /same angle parameters as: CT C N 1 116.600 585.760 ; AA general NQ C O 1 122.900 669.440 ; new amber99sb-ucb,ASN,GLN /same angle parameters as: N C O 1 122.900 669.440 ; AA general
2)LYN (neutral LYS) HP CT NQ 1 109.500 418.400 ; new amber99sb-ucb,LYN(neutral LYS) /same angle parameters as: HP CT N 1 109.500 418.400 ; AA lys, ch3nh3+, changed based on NMA nmodes CT CT NQ 1 111.200 669.440 ; new amber99sb-ucb,LYN(neutral LYS) /same angle parameters as: CT CT N 1 111.200 669.440 ; AA lys (JCP 76, 1439) CT NQ HQ 1 109.500 418.400 ; new amber99sb-ucb,LYN(neutral LYS) /same angle parameters as: CT N H 1 109.500 418.400 ; AA lys, changed based on NMA nmodes HQ NQ HQ 1 120.000 292.880 ; new amber99sb-ucb,LYN(neutral LYS) /same angle parameters as: H N H 1 109.500 292.880 ; AA lys, AA(end)
3)TYR CA C OR 1 120.000 585.760 ; new amber99sb-ucb,TYR /same angle parameters as: CA C OH 1 120.000 585.760 ; AA tyr C OR HO 1 113.000 418.400 ; new amber99sb-ucb,TYR /same angle parameters as: C OH HO 1 113.000 418.400 ; new99
add new angles to ffbonded.itp: #DONE!
C NQ HQ 1 120.000 418.400 ; new amber99sb-ucb,ASN,GLN
CT C NQ 1 116.600 585.760 ; new amber99sb-ucb,ASN,GLN
NQ C O 1 122.900 669.440 ; new amber99sb-ucb,ASN,GLN
HQ NQ HQ 1 120.000 292.880 ; new amber99sb-ucb,ASN,GLN,LYN(neutral LYS)
HP CT NQ 1 109.500 418.400 ; new amber99sb-ucb,LYN(neutral LYS)
CT CT NQ 1 111.200 669.440 ; new amber99sb-ucb,LYN(neutral LYS)
CT NQ HQ 1 109.500 418.400 ; new amber99sb-ucb,LYN(neutral LYS)
CA C OR 1 120.000 585.760 ; new amber99sb-ucb,TYR
C OR HO 1 113.000 418.400 ; new amber99sb-ucb,TYR
######### New propers dihederals ############## New propers dihederals:
1)ASN and GLN CT C NQ HQ define as: X C NQ X 9 180.0 10.46000 2 ; new amber99sb-ucb,ASN,GLN /same propers dih parameters as: X C N X 9 180.0 10.46000 2 ; AA,NMA O C NQ HQ define as: X C NQ X 9 180.0 10.46000 2 ; new amber99sb-ucb,ASN,GLN /same propers dih parameters as: X C N X 9 180.0 10.46000 2 ; AA,NMA
2)LYN (neutral LYS) CT CT NQ HQ define as: X CT NQ X 9 0.0 0.65084 3 ; new amber99sb-ucb,LYN /same propers dih parameters as: X CT N3 X 9 0.0 0.65084 3 ; JCC,7,(1986),230 HP CT NQ HQ define as: X CT NQ X 9 0.0 0.65084 3 ; new amber99sb-ucb,LYN /same propers dih parameters as: X CT N3 X 9 0.0 0.65084 3 ; JCC,7,(1986),230
3)TYR CA C OR HO define as: X C OR X 9 180.0 9.62320 2 ; new amber99sb-ucb,TYR /same propers dih parameters as: X C OH X 9 180.0 9.62320 2 ; Junmei et al, 1999
add new propers dihederals to ffbonded.itp: #DONE!
X C NQ X 9 180.0 10.46000 2 ; new amber99sb-ucb,ASN,GLN X C NQ X 9 180.0 10.46000 2 ; new amber99sb-ucb,ASN,GLN X CT NQ X 9 0.0 0.65084 3 ; new amber99sb-ucb,LYN(neutral LYS) X C OR X 9 180.0 9.62320 2 ; new amber99sb-ucb,TYR
######### New impropers dihederals ##############
1)ASN and GLN:(form aminoasids.rtp file)
impropers for ASN form aminoasids.rtp file:
CB ND2 CG OD1: define new improper dih CT NQ C O, same impropers dih parameters as CT N C O
CG HD21 ND2 HD22: define new improper dih C HQ NQ HQ, same impropers dih parameters as C H N H
impropers for GLN form aminoasids.rtp file:
CG NE2 CD OE1: define new improper dih CT NQ C O, same impropers dih parameters as CT N C O
CD HE21 NE2 HE22: define new improper dih C HQ NQ HQ, same impropers dih parameters as C H N H
improper dih CT N C O in ffbonded.itp define as: X X C O 4 180.00 43.93200 2 ; JCC,7,(1986),230 /## no need to add it ## improper dih C H N H in ffbonded.itp define as: X X N H 4 180.00 4.18400 2 ; JCC,7,(1986),230
2)TYR CA CA C OR 4 180.00 4.60240 2 ; new amber99sb-ucb,TYR /same impropers parameters as: CA CA C OH 4 180.00 4.60240 2
add new impropers dih to ffbonded.itp: #DONE!
X X NQ HQ 4 180.00 4.18400 2 ; new amber99sb-ucb,ASN,GLN CA CA C OR 4 180.00 4.60240 2 ; new amber99sb-ucb,TYR
################################################################################## edit ffbonded.itp (added to avoid errors in gmx grompp)
HQ 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 ; new amber99sb-ucb;ASN,GLN,LYN(neutral LYS) /same parameters as H NQ 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 ; new amber99sb-ucb;ASN,GLN,LYN(neutral LYS) /same parameters as N OR 8 16.00 0.0000 A 3.06647e-01 8.80314e-01 ; new amber99sb-ucb;TYR /same parameters as OH
################################################################################ create new file nbfix.itp
################################################################################## ########## Partial atomic charges ######### change the partial atomic charges for C-terminus non-protonated ALA, GLY, and VAL. The data from SI Table 8 (https://doi.org/10.1021/ct2000183):
aminoacids.rtp
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CALA [ atoms ] N N -0.43970 1 ; new amber99sb-ucb H H 0.26110 2 ; new amber99sb-ucb CA CT 0.06060 3 ; new amber99sb-ucb HA H1 0.08790 4 ; new amber99sb-ucb CB CT -0.10780 5 ; new amber99sb-ucb HB1 HC 0.04180 6 ; new amber99sb-ucb HB2 HC 0.04180 7 ; new amber99sb-ucb HB3 HC 0.04180 8 ; new amber99sb-ucb C C 0.83290 9 ; new amber99sb-ucb OC1 O2 -0.60740 10 ; new amber99sb-ucb OC2 O2 -0.66320 11 ; new amber99sb-ucb
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CGLY [ atoms ] N N -0.37180 1 ; new amber99sb-ucb H H 0.25810 2 ; new amber99sb-ucb CA CT -0.11370 3 ; new amber99sb-ucb HA1 H1 0.09270 4 ; new amber99sb-ucb HA2 H1 0.09270 5 ; new amber99sb-ucb C C 0.87960 6 ; new amber99sb-ucb OC1 O2 -0.61740 7 ; new amber99sb-ucb OC2 O2 -0.66550 8 ; new amber99sb-ucb
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CVAL [ atoms ] N N -0.33850 1 ; new amber99sb-ucb H H 0.22970 2 ; new amber99sb-ucb CA CT -0.09100 3 ; new amber99sb-ucb HA H1 0.10340 4 ; new amber99sb-ucb CB CT 0.20170 5 ; new amber99sb-ucb HB HC -0.00380 6 ; new amber99sb-ucb CG1 CT -0.19790 7 ; new amber99sb-ucb HG11 HC 0.04710 8 ; new amber99sb-ucb HG12 HC 0.04710 9 ; new amber99sb-ucb HG13 HC 0.04710 10 ; new amber99sb-ucb CG2 CT -0.19790 11 ; new amber99sb-ucb HG21 HC 0.04710 12 ; new amber99sb-ucb HG22 HC 0.04710 13 ; new amber99sb-ucb HG23 HC 0.04710 14 ; new amber99sb-ucb C C 0.83150 15 ; new amber99sb-ucb OC1 O2 -0.60710 16 ; new amber99sb-ucb OC2 O2 -0.66310 17 ; new amber99sb-ucb
Reverting the partial charges of CVAL, CGLY, CALA back to the original A99disp, as they are not protonated and their charges are not supposed to be changed.
Changed O2 atom type in CVAH, CGLH, and CALH to O. Apparently this is the correct version.
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