[gmx-users] Confusion regarding creation of .itp file

[Apramita Chand]

Hello,
I'm a beginner in GROMACS and have been trying to process small molecule
topologies through GROMACS for quite sometime. Initially while adding new
residues , I thought it's better to modify forcefield files such as
ffnonbonded.itp, residuetypes.dat, .rtp entries. However, I've seen in many
places that it is better if the new molecules are just added to the master
topology file by creating .itp files.
To give me a better feel of how .itp files look like, I downloaded .itp
file of urea from ATB server( for use with GROMOS96 53a6) and included it
in my system and it worked. However, the real problem is that I've looked
up the parameters of urea from this paper:
http://pubs.acs.org/doi/pdf/10.1021/jp030534x
for use with GROMOS96 forcefield and I have the .xyz coordinate file.
So now I'm trying to modify the .itp file that I downloaded from the server
to suit the parameters in the paper.
the .itp file looks like:
;
[ moleculetype ]
; Name   nrexcl
HF0U     3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1  HS14    1    HF0U     H6    1    0.426   1.0080
    2    NT    1    HF0U     N1    1   -0.981  14.0067
    3  HS14    1    HF0U     H5    1    0.426   1.0080
    4     C    1    HF0U     C2    1    0.915  12.0110
    5     O    1    HF0U     O4    1   -0.657  15.9994     ;  0.129
    6    NT    1    HF0U     N3    2   -0.981  14.0067
    7  HS14    1    HF0U     H7    2    0.426   1.0080
    8  HS14    1    HF0U     H8    2    0.426   1.0080     ; -0.129
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0         c1
    1    2    2   0.1010   2.1076e+07
    2    3    2   0.1010   2.1076e+07
    2    4    2   0.1380   1.1000e+07
    4    5    2   0.1230   1.6600e+07
    4    6    2   0.1380   1.1000e+07
    6    7    2   0.1010   2.1076e+07
    6    8    2   0.1010   2.1076e+07
[ pairs ]
;  ai   aj  funct  ;  all 1-4 pairs but the ones excluded in GROMOS itp
    1    5    1
    1    6    1
    2    7    1
    2    8    1
    3    5    1
    3    6    1
    5    7    1
    5    8    1
[ angles ]
;  ai   aj   ak  funct   angle     fc
    1    2    3    2    113.00   545.00
    1    2    4    2    115.00   460.00
    3    2    4    2    115.00   460.00
    2    4    5    2    124.00   730.00
    2    4    6    2    120.00   560.00
    5    4    6    2    124.00   730.00
    4    6    7    2    115.00   460.00
    4    6    8    2    115.00   460.00
    7    6    8    2    113.00   545.00
[ dihedrals ]
; GROMOS improper dihedrals
;  ai   aj   ak   al  funct   angle     fc
    4    2    6    5    2      0.00   167.36
[ dihedrals ]
;  ai   aj   ak   al  funct    ph0      cp     mult
    1    2    4    5    1    180.00     5.86    2
    5    4    6    8    1    180.00     5.86    2
[ exclusions ]
;  ai   aj  funct  ;  GROMOS 1-4 exclusions


I'm really confused about the various terms like 'ai,aj,ak,al', 'funct',
'c0,c1', 'cp' 'mult'
How is the 'pairs' category constructed.
I referred to the GROMACS manual 4.6.5 but did not find a concrete
explanation.

Further, I would like to know if I'm following the proper procedure.



I would really appreciate your help.

Regards,
Apramita