Amber99SBNMR1
- Force filed is included in Amber12.
- For other version of Amber:
- Download frcmod.ff99SBnmr and put it into your amberhome/dat/leap/parm folder
- 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:
- Download frcmod.ff99SBnmr and put it into your amberhome/dat/leap/parm folder
- 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