*>>>>>> All-hydrogen topology for neutral Arg <<<<<<<<<<<<<<<<<<<<
*>>>>>>>>>>>>>>>>>>>>>>> 2007 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
*>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<<
*>>>>>>>>>>>>>>> Parameter forum, www.charmm.org <<<<<<<<<<<<<<<<<
*

! Atom names include "R" (for Arg) as the second letter. The
! only other atom types in the additive FF with this second
! letter are histidine [HN]R[123] in the protein FF and CRL[12]
! in toppar_all36_lipid_cholesterol.str , so no more conflicts.

!Parent files that have to be read prior to streaming this file
!top_all36_prot.rtf
!par_all36_prot.rtf
!
!Testcase
!test_all36_prot_arg0.inp

!Li, L., Vorobyov, I.V., MacKerell, Jr., A.D., Allen, T.W., "Is
!arginine charged in a membrane?" Biophysical Journal, 94: L11-L13,
!2008, PMCID: PMC2157258

read rtf card append
* Topology for protein related model compounds
*
31  1

! use flexible toplogy/parameter reader
!!atom for methylguanidine compounds
!!atoms renamed to 4 letter code
MASS  -1  HRA3       1.00800 ! alphatic proton, CH3
MASS  -1  HRP2       1.00800 ! polar H, +ve charge
MASS  -1  HRM1       1.00800 ! polar H, dimethylamine
MASS  -1  HRM2       1.00800 ! polar H, methylamine
MASS  -1  CRN1      12.01100 ! conjugated C in Arg/guanidinium
MASS  -1  CR33      12.01100 ! aliphatic C for methyl group (-CH3)
MASS  -1  NRC4      14.00700 ! N for deprotonated Schiff's base
MASS  -1  NRN1      14.00700 ! dimethylamine nitrogen
MASS  -1  NRN2      14.00700 ! methylamine nitrogen


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!! original topology from Alex
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


!methylguanidine model compounds
RESI MGU1          0.00 ! deprotonated methyl-guanidinium
                        ! Ne deprotonated
GROUP  
ATOM  C   CRN1     0.66 !      H11  H12
ATOM  N1  NRN2    -0.60 !        \  /
ATOM  H11 HRM2     0.29 !         N1
ATOM  H12 HRM2     0.29 !         |
ATOM  N2  NRN2    -0.60 !         C       H41
ATOM  H21 HRM2     0.29 !        / \\    /
ATOM  H22 HRM2     0.29 !  H21-N2   N3--C4-H42
ATOM  N3  NRC4    -0.86 !       |        \
ATOM  C4  CR33    -0.03 !     H22         H43   !extra charge on C4 to neutralize
ATOM  H41 HRA3     0.09
ATOM  H42 HRA3     0.09
ATOM  H43 HRA3     0.09
BOND   C  N1   C N2    C N3     N3 C4
BOND   N1 H11  N1 H12  N2 H21   N2 H22  
BOND   C4 H41  C4 H42  C4 H43
IMPR   C  N2  N1  N3 
IMPR   N1 H11 H12 C  N2 H21 H22 C

IC C4   N3   C    N1     0.0000    0.00  180.00    0.00   0.0000
IC N1   N3   *C   N2     0.0000    0.00  180.00    0.00   0.0000
IC N3   C    N1   H11    0.0000    0.00  180.00    0.00   0.0000
IC H11  C    *N1  H12    0.0000    0.00  180.00    0.00   0.0000
IC N3   C    N2   H21    0.0000    0.00  180.00    0.00   0.0000
IC H21  C    *N2  H22    0.0000    0.00  180.00    0.00   0.0000
IC N1   C    N3   C4     0.0000    0.00  180.00    0.00   0.0000
IC C    N3   C4   H41    0.0000    0.00  180.00    0.00   0.0000
IC H41  N3   *C4  H42    0.0000    0.00  120.00    0.00   0.0000
IC H41  N3   *C4  H43    0.0000    0.00 -120.00    0.00   0.0000
patc firs none last none

RESI MGU2          0.00 ! deprotonated methyl-guanidinium
                        ! NH1-H12 (outer) deprotonated
GROUP               
ATOM  C   CRN1     0.59 !
ATOM  N1  NRC4    -0.91 !      H11
ATOM  H11 HRP2     0.37 !        \
ATOM  N2  NRN2    -0.60 !         N1 
ATOM  H21 HRM2     0.33 !         ||
ATOM  H22 HRM2     0.33 !         C       H41
ATOM  N3  NRN1    -0.54 !        / \     /
ATOM  H31 HRM1     0.36 !  H21-N2   N3--C4-H42
ATOM  C4  CR33    -0.20 !       |   |    \      !carbon charge to neutralize
ATOM  H41 HRA3     0.09 !     H22   H31   H43
ATOM  H42 HRA3     0.09
ATOM  H43 HRA3     0.09
BOND   C  N1   C  N2    C N3    N3 C4
BOND   N1 H11  N2 H21   N2 H22  N3 H31
BOND   C4 H41  C4 H42   C4 H43
IMPR   C  N2  N1  N3
IMPR   N3 C4  C   H31  N2 H21 H22 C

IC C4   N3   C    N1     0.0000    0.00  180.00    0.00   0.0000
IC N1   N3   *C   N2     0.0000    0.00  180.00    0.00   0.0000
IC N3   C    N1   H11    0.0000    0.00  180.00    0.00   0.0000
IC N3   C    N2   H21    0.0000    0.00  180.00    0.00   0.0000
IC H21  C    *N2  H22    0.0000    0.00  180.00    0.00   0.0000
IC N1   C    N3   C4     0.0000    0.00  180.00    0.00   0.0000
IC C    C4   *N3  H31    0.0000    0.00  180.00    0.00   0.0000
IC C    N3   C4   H41    0.0000    0.00  180.00    0.00   0.0000
IC H41  N3   *C4  H42    0.0000    0.00  120.00    0.00   0.0000
IC H41  N3   *C4  H43    0.0000    0.00 -120.00    0.00   0.0000

patc firs none last none

RESI MGU3          0.00 ! deprotonated methyl-guanidinium
                        ! NH1-H11 (inner) deprotonated
!
!MGU3 parameters obtained directly from MGU2 optimization
!charges readjust to improve interactions with water
!Two charge models determined with and without IMPRoper
!on H31 atom, which has a large effect on the pyramidalization
!and the overall dipole moment
!
!charges with !IMPR   N3 C4  C   H31 commented out
GROUP  
ATOM  C   CRN1     0.59 !
ATOM  N1  NRC4    -0.95 !           H12
ATOM  H12 HRP2     0.33 !           /
ATOM  N2  NRN2    -0.60 !         N1 
ATOM  H21 HRM2     0.33 !         ||
ATOM  H22 HRM2     0.33 !         C       H41
ATOM  N3  NRN1    -0.54 !        / \     /
ATOM  H31 HRM1     0.44 !  H21-N2   N3--C4-H42
ATOM  C4  CR33    -0.20 !       |   |    \      
ATOM  H41 HRA3     0.09 !     H22   H31   H43
ATOM  H42 HRA3     0.09
ATOM  H43 HRA3     0.09

!charges with !IMPR   N3 C4  C   H31 included
!GROUP
!ATOM  C   CRN1     0.59 !
!ATOM  N1  NRC4    -1.01 !           H12
!ATOM  H12 HRP2     0.39 !           /
!ATOM  N2  NRN2    -0.56 !         N1 
!ATOM  H21 HRM2     0.33 !         ||
!ATOM  H22 HRM2     0.33 !         C       H41
!ATOM  N3  NRN1    -0.55 !        / \     /
!ATOM  H31 HRM1     0.41 !  H21-N2   N3--C4-H42
!ATOM  C4  CR33    -0.20 !       |   |    \      
!ATOM  H41 HRA3     0.09 !     H22   H31   H43
!ATOM  H42 HRA3     0.09
!ATOM  H43 HRA3     0.09
BOND   C  N1   C  N2   C  N3    N3 C4
BOND   N1 H12  N2 H21   N2 H22  N3 H31
BOND   C4 H41 C4 H42 C4 H43
IMPR   C  N2  N1  N3
!IMPR   N3 C4  C   H31 
IMPR   N2 H21 H22 C

IC C4   N3   C    N1     0.0000    0.00  180.00    0.00   0.0000
IC N1   N3   *C   N2     0.0000    0.00  180.00    0.00   0.0000
IC N3   C    N1   H12    0.0000    0.00    0.00    0.00   0.0000
IC N3   C    N2   H21    0.0000    0.00  180.00    0.00   0.0000
IC H21  C    *N2  H22    0.0000    0.00  180.00    0.00   0.0000
IC N1   C    N3   C4     0.0000    0.00  180.00    0.00   0.0000
IC C    C4   *N3  H31    0.0000    0.00  180.00    0.00   0.0000
IC C    N3   C4   H41    0.0000    0.00  180.00    0.00   0.0000
IC H41  N3   *C4  H42    0.0000    0.00  120.00    0.00   0.0000
IC H41  N3   *C4  H43    0.0000    0.00 -120.00    0.00   0.0000
patc firs none last none

!patches to convert arginine to neutral species based on the
!methylguanidine model compounds
PRES RN1          0.00 !patch for neutral arginine: He delete
DELE ATOM HE           !from RESI MGU1
GROUP   
ATOM CD   CT2      0.06 !-0.03
ATOM HD1  HA2      0.09
ATOM HD2  HA2      0.09
ATOM NE   NRC4    -0.86
ATOM CZ   CRN1     0.66
ATOM NH1  NRN2    -0.60
ATOM HH11 HRM2     0.29
ATOM HH12 HRM2     0.29
ATOM NH2  NRN2    -0.60
ATOM HH21 HRM2     0.29
ATOM HH22 HRM2     0.29
!IMPR   C  N2  N1  N3 !present in RESI ARG
IMPR NH1 HH11 HH12 CZ
IMPR NH2 HH21 HH22 CZ

PRES RN2          0.00 !patch for neutral arginine: HH12 deleted (proton removed from NH2)
DELE ATOM HH12         !from RESI MGU2
GROUP
ATOM CD   CT2     -0.11 ! -0.20
ATOM HD1  HA2      0.09
ATOM HD2  HA2      0.09
ATOM NE   NRN1    -0.54
ATOM HE   HRM1     0.36
ATOM CZ   CRN1     0.59
ATOM NH1  NRC4    -0.91
ATOM HH11 HRP2     0.37
ATOM NH2  NRN2    -0.60
ATOM HH21 HRM2     0.33
ATOM HH22 HRM2     0.33
IMPR NE  CD   CZ   HE
IMPR NH2 HH21 HH22 CZ

PRES RN3          0.00 !patch for neutral arginine: HH12 deleted (proton adjacent to NH2)
DELE ATOM HH11         !from RESI MGU3 (see comments on MGU3 residue above)
GROUP
ATOM CD   CT2     -0.11 ! -0.20
ATOM HD1  HA2      0.09
ATOM HD2  HA2      0.09
ATOM NE   NRN1    -0.54
ATOM HE   HRM1     0.44
ATOM CZ   CRN1     0.59
ATOM NH1  NRC4    -0.95
ATOM HH12 HRP2     0.33
ATOM NH2  NRN2    -0.60
ATOM HH21 HRM2     0.33
ATOM HH22 HRM2     0.33
!IMPR NE  CD   CZ   HE  !removed based on MGU3, see above
IMPR NH2 HH21 HH22 CZ

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!! The topology below is from
!!!!  the group of Toby Allen
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!! propyl guanidine
!! based on MGU1 and RN1
!! note different atom naming
!! and numbering

!reset default patches

DEFA FIRS NONE LAST NONE

!following not tested

RESI PGUN          0.00
GROUP
ATOM CB   CT3    -0.27  !
ATOM HB1  HA3     0.09  !
ATOM HB2  HA3     0.09  !
ATOM HB3  HA3     0.09
GROUP                   !
ATOM CG   CT2    -0.18
ATOM HG1  HA2     0.09
ATOM HG2  HA2     0.09
GROUP
ATOM CD   CT2      0.06 !-0.03
ATOM HD1  HA2      0.09
ATOM HD2  HA2      0.09
ATOM NE   NRC4    -0.86
!ATOM HE   DUM      0.00
ATOM CZ   CRN1     0.66
ATOM NH1  NRN2    -0.60
ATOM HH11 HRM2     0.29
ATOM HH12 HRM2     0.29
ATOM NH2  NRN2    -0.60
ATOM HH21 HRM2     0.29
ATOM HH22 HRM2     0.29

BOND CG  CB  CD CG  NE CD  CZ NE
BOND NH2 CZ
BOND CB  HB3  CB HB1
BOND CB  HB2 CG  HG1 CG HG2 CD HD1 CD HD2
BOND NH1 HH11  NH1 HH12  NH2 HH21  NH2 HH22
DOUBLE   CZ  NH1
IMPR CZ NH1 NH2 NE
IMPR NH1 HH11 HH12 CZ
IMPR NH2 HH21 HH22 CZ
ACCEPTOR NE
DONOR HH11 NH1
DONOR HH12 NH1
DONOR HH21 NH2
DONOR HH22 NH2

!! Methyl guanidine residue
!! based on MGU1 and RN1
!! note different atom naming
!! and numbering

RESI MGUN          0.00
GROUP
ATOM CD   CT2     -0.03
ATOM HD1  HA2      0.09
ATOM HD2  HA2      0.09
ATOM HD3  HA2      0.09
ATOM NE   NRC4    -0.86
!ATOM HE   DUM      0.00
ATOM CZ   CRN1     0.66
ATOM NH1  NRN2    -0.60
ATOM HH11 HRM2     0.29
ATOM HH12 HRM2     0.29
ATOM NH2  NRN2    -0.60
ATOM HH21 HRM2     0.29
ATOM HH22 HRM2     0.29

BOND NE CD  CZ NE
BOND NH2 CZ
BOND CD HD1 CD HD2  CD HD3
BOND NH1 HH11  NH1 HH12  NH2 HH21  NH2 HH22
DOUBLE   CZ  NH1
IMPR CZ NH1 NH2 NE
IMPR NH1 HH11 HH12 CZ
IMPR NH2 HH21 HH22 CZ
ACCEPTOR NE
DONOR HH11 NH1
DONOR HH12 NH1
DONOR HH21 NH2
DONOR HH22 NH2


PATCHING FIRST NONE LAST NONE

END

read param card flex append

ATOMS
MASS  -1  HRA3       1.00800 ! alphatic proton, CH3
MASS  -1  HRP2       1.00800 ! polar H, +ve charge
MASS  -1  HRM1       1.00800 ! polar H, dimethylamine
MASS  -1  HRM2       1.00800 ! polar H, methylamine
MASS  -1  CRN1      12.01100 ! conjugated C in Arg/guanidinium
MASS  -1  CR33      12.01100 ! aliphatic C for methyl group (-CH3)
MASS  -1  NRC4      14.00700 ! N for deprotonated Schiff's base
MASS  -1  NRN1      14.00700 ! dimethylamine nitrogen
MASS  -1  NRN2      14.00700 ! methylamine nitrogen

BONDS
!atom type Kb          b0
!methylguanidine
!new parameters
CRN1   NRC4    500.00     1.3100 ! MGU1, methylguanidine
CRN1   NRN2    450.00     1.4400 ! MGU1, methylguanidine
!
CRN1   NRN1    500.00     1.4400 ! MGU2, methylguanidine2
CR33   NRN1    255.00     1.4630 ! MGU2, methylguanidine2
NRC4   HRP2    455.00     1.0000 ! MGU2, methylguanidine2
!transferred parameters
CR33   NRC4    310.00     1.4400 ! RETINOL SCH1, Schiff's base, deprotonated
CR33   HRA3    322.00     1.1110 ! PROT alkane update, adm jr., 3/2/92
NRN1   HRM1    447.80     1.0190 ! AMINE aliphatic amines
NRN2   HRM2    453.10     1.0140 ! AMINE aliphatic amines
NRN1   CT2     255.00     1.4630 ! MGU2, methylguanidine2
NRC4   CT2     310.00     1.4400 ! RETINOL SCH1, Schiff's base, deprotonated
!end methylguanidine


ANGLES
!atom types     Ktheta    Theta0   Kub     S0
!methylguanidine
!new parameters
NRN2   CRN1   NRN2     75.00    113.00 ! MGU1, methylguanidine
NRN2   CRN1   NRC4    100.00    125.00 ! MGU1, methylguanidine
CRN1   NRC4   CR33     50.00    108.00 ! MGU1, methylguanidine
CRN1   NRN2   HRM2     55.00    108.00 ! MGU1, methylguanidine
!
NRC4   CRN1   NRN1     50.00    125.00 ! MGU2, methylguanidine2
NRN2   CRN1   NRN1     50.00    110.00 ! MGU2, methylguanidine2
CRN1   NRN1   CR33     43.00    106.00 ! MGU2, methylguanidine2
CRN1   NRN1   HRM1     45.00    104.00 ! MGU2, methylguanidine2
CR33   NRN1   HRM1     45.00    104.00 ! MGU2, methylguanidine2
NRN1   CR33   HRA3     30.50    109.70   50.00   2.1400 ! MGU2, methylguanidine2
CRN1   NRC4   HRP2     49.00    113.00 ! MGU2, methylguanidine2
!transferred parameters
NRC4   CR33   HRA3     42.00    113.50 ! RETINOL SCH1, Schiff's base, deprotonated
HRM2   NRN2   HRM2     29.50    105.85 ! AMINE aliphatic amines
HRA3   CR33   HRA3     35.50    108.40    5.40   1.80200 ! PROT alkane update
CT2    CT2    NRC4     67.70    110.00 ! RETINOL SCK0, deprotonated Schiff's base
HA2    CT2    NRC4     42.00    113.50 ! RETINOL SCK0, deprotonated Schiff's base
CT2    NRC4   CRN1     50.00    108.00 ! MGU1, methylguanidine
CT2    CT2    NRN1     67.70    107.50 ! PROT arg, (DS)
HA2    CT2    NRN1     30.50    109.70   50.00   2.1400 ! MGU2, methylguanidine2
CT2    NRN1   HRM1     45.00    104.00 ! MGU2, methylguanidine2
CT2    NRN1   CRN1     43.00    106.00 ! MGU2, methylguanidine
!end methylguanidine

DIHEDRALS
!atom types             Kchi    n   delta
!
!methylguanidine
!new parameters
CRN1   NRC4   CR33   HRA3      0.1100  3   180.00 ! MGU1, methylguanidine
NRN2   CRN1   NRC4   CR33      6.5000  2   180.00 ! MGU1, methylguanidine
NRC4   CRN1   NRN2   HRM2      1.3000  3   180.00 ! MGU1, methylguanidine
NRN2   CRN1   NRN2   HRM2      1.3000  3   180.00 ! MGU1, methylguanidine
!
NRC4   CRN1   NRN1   CR33       0.5000  2   180.00 ! MGU2, methylguanidine2
NRN2   CRN1   NRN1   CR33       0.5000  2   180.00 ! MGU2, methylguanidine2
HRP2   NRC4   CRN1   NRN2       5.2000  2   180.00 ! MGU2, methylguanidine2
HRP2   NRC4   CRN1   NRN1       5.2000  2   180.00 ! MGU2, methylguanidine2
HRM2   NRN2   CRN1   NRN1       1.3000  3   180.00 ! MGU2, methylguanidine2
NRC4   CRN1   NRN1   HRM1       2.8000  3   180.00 ! MGU2, methylguanidine2
NRN2   CRN1   NRN1   HRM1       2.8000  3   180.00 ! MGU2, methylguanidine2
CRN1   NRN1   CR33   HRA3       0.0000  3   180.00 ! MGU2, methylguanidine2
HRM1   NRN1   CR33   HRA3       0.4200  3     0.00 ! MGU2, methylguanidine2
!transferred parameters
CT2    CT2    NRC4   CRN1       0.1000  3     0.00 ! RETINOL SCH1, Schiff's base, deprotonated
CT2    NRC4   CRN1   NRN2       6.5000  2   180.00 ! MGU1, methylguanidine
HA2    CT2    NRC4   CRN1       0.1100  3   180.00 ! MGU1, methylguanidine
CT2    CT2    NRN1   HRM1       0.3000  3   180.00 ! amines
CT2    CT2    NRN1   CRN1       0.3000  3   180.00 ! amines
CT2    NRN1   CRN1   NRC4       0.5000  2   180.00 ! MGU2, methylguanidine2
HA2    CT2    NRN1   HRM1       0.4200  3     0.00 ! MGU2, methylguanidine2
HA2    CT2    NRN1   CRN1       0.0000  3   180.00 ! MGU2, methylguanidine2
CT2    NRN1   CRN1   NRN2       0.5000  2   180.00 ! MGU2, methylguanidine2
!end methylguanidine

IMPROPER
!atom types           Kpsi                   psi0
!methylguanidine
CRN1   NRN2   NRN2   NRC4    170.0000  1   180.00 ! MGU1, methylguanidine
NRN2   HRM2   HRM2   CRN1     40.0000  1   180.00 ! MGU1, methylguanidine
!
CRN1   NRN2   NRC4   NRN1    170.0000  1   180.00 ! MGU2, methylguanidine2
NRN1   CR33   CRN1   HRM1     60.0000  1   180.00 ! MGU2, methylguanidine2
!transferred parameters
CRN1   NRC4   NRN2   NRN1    170.0000  1   180.00 ! MGU1, methylguanidine
NRN1   CT2    CRN1   HRM1     60.0000  1   180.00 ! MGU2, methylguanidine2
!end methylguanidine

NONBONDED nbxmod  5 atom cdiel fshift vatom vdistance vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
                !adm jr., 5/08/91, suggested cutoff scheme
!methylguanidine parameters
HRA3     0.0       -0.0240     1.3400 ! alkane, yin and mackerell, 4/98
HRP2     0.0       -0.0460     0.2245 ! small polar Hydrogen, charged systems
HRM1     0.0       -0.0090     0.8750 ! aliphatic amines
HRM2     0.0       -0.0100     0.8750 ! aliphatic amines
!
CRN1     0.0       -0.1100     2.0000 ! NMA pure solvent, adm jr., 3/3/93
CR33     0.0       -0.0780     2.0500   0.0 -0.01 1.9 ! alkane (CT3), 4/98, yin, adm jr
!
NRC4     0.0       -0.2000     1.8500 ! deprotonated Schiff's base
NRN1     0.0       -0.4500     2.0000 ! aliphatic amines
NRN2     0.0       -0.0600     1.9900 ! aliphatic amines
!end methylguanidine

end

return
