Protein force fields

Amber99SBNMR1

  • Force filed is included in Amber12.
  • For other version of Amber:
    1. Download frcmod.ff99SBnmr and put it into your amberhome/dat/leap/parm folder
    2. Run command “loadamberparams frcmod.ff99SBnmr” after load in ff99SB and before build your topology in tleap.
  • For Gromacs 4.5 and higher, download the package to Gromacs/top then untar

Amber99SBNMR1-ILDN

  • For Gromacs 4.5 and higher, download the package to Gromacs/top then untar
  • For Amber:
    1. Download frcmod.ff99SBnmr and put it into your amberhome/dat/leap/parm folder
    2. Run command “loadamberparams frcmod.ff99SBnmr”after load in ff99SBildn and before build your topology in tleap.

Amber99SBNMR2 (with ILDN)

  • For Gromacs 5 and higher, download the package then follow instructions.

Amber99SB_ΦΨ(G24,CS)

Instructions: Download the cmap.itp file to you working directory then modify your top file generated by pdb2gmx program of gromacs in two steps.

1 add #include “./cmap.itp” after the line that include the forcefield paramters (A line that read #include “amber99sb-ildn.ff/forcefield.itp”).
2 add a new section after the dihedral section like this:

[ cmap ]
18          20          22          30          32
30          32          34          41          43
………….

Each line in this section have 5 numbers, which are the atom index  of C_i-1,
N_i, Ca_i, C_i, N_i+1 that define one particular phi-psi plane. You need to add
all phi-psi plane. Atom indexs can be obtained from the [ atoms ] section of
the top file.

The dihedral section looks like this

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3
5    20    18    19     4
18    22    20    21     4
22    32    30    31     4
24    28    27    29     4
30    34    32    33     4

the atoms section looks like this

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
; residue   1 MET rtp NMET q +1.0
1         N3      1    MET      N      1     0.1592      14.01   ; qtot 0.1592
2          H      1    MET     H1      2     0.1984      1.008   ; qtot 0.3576
3          H      1    MET     H2      3     0.1984      1.008   ; qtot 0.556
4          H      1    MET     H3      4     0.1984      1.008   ; qtot 0.7544
5         CT      1    MET     CA      5     0.0221      12.01   ; qtot 0.7765
6         HP      1    MET     HA      6     0.1116      1.008   ; qtot 0.8881
7         CT      1    MET     CB      7     0.0865      12.01   ; qtot 0.9746
8         HC      1    MET    HB1      8     0.0125      1.008   ; qtot 0.9871
9         HC      1    MET    HB2      9     0.0125      1.008   ; qtot 0.9996
10         CT      1    MET     CG     10     0.0334      12.01   ; qtot 1.033
11         H1      1    MET    HG1     11     0.0292      1.008   ; qtot 1.062
12         H1      1    MET    HG2     12     0.0292      1.008   ; qtot 1.091
13          S      1    MET     SD     13    -0.2774      32.06   ; qtot 0.814
14         CT      1    MET     CE     14    -0.0341      12.01   ; qtot 0.7799

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