GROMACS version: 2025.1
GROMACS modification: No
Hello, my name is Matias Romero. I’m working with Gromacs for my thesis studies last year, but I’m stuck in a big problem. I have a big problem trying to modify a topology file. This is because my thesis is trying to add a correction in the order of C6 from the LJ potential. I try to generate manually my [ nonbond_params ] of a topology generated from AMBER and transform in to GROMACS structure by using ACPYPE. With this I was able to differentiate the atom type of the same molecule but as a different enantiomer, this is my atom type structure.
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333333333
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
c3 c3 0.00000 0.00000 A 3.39771e-01 4.51035e-01 ; 1.91 0.1078
ca ca 0.00000 0.00000 A 3.31521e-01 4.13379e-01 ; 1.86 0.0988
cp cp 0.00000 0.00000 A 3.31521e-01 4.13379e-01 ; 1.86 0.0988
cg cg 0.00000 0.00000 A 3.47896e-01 6.67766e-01 ; 1.95 0.1596
n1 n1 0.00000 0.00000 A 3.27352e-01 4.59403e-01 ; 1.84 0.1098
hc hc 0.00000 0.00000 A 2.60018e-01 8.70272e-02 ; 1.46 0.0208
ha ha 0.00000 0.00000 A 2.62548e-01 6.73624e-02 ; 1.47 0.0161
c4 c4 0.00000 0.00000 A 3.39771e-01 4.51035e-01 ; 1.91 0.1078
cb cb 0.00000 0.00000 A 3.31521e-01 4.13379e-01 ; 1.86 0.0988
cq cq 0.00000 0.00000 A 3.31521e-01 4.13379e-01 ; 1.86 0.0988
ch ch 0.00000 0.00000 A 3.47896e-01 6.67766e-01 ; 1.95 0.1596
n2 n2 0.00000 0.00000 A 3.27352e-01 4.59403e-01 ; 1.84 0.1098
hd hd 0.00000 0.00000 A 2.60018e-01 8.70272e-02 ; 1.46 0.0208
hb hb 0.00000 0.00000 A 2.62548e-01 6.73624e-02 ; 1.47 0.0161
The Forcefiel is GAFF2, and I try to generate the [ nonbond_params ] by using the Gromacs manual (page 458) , to generate the parameters. But it didn’t work. I know that the non-bonding parameters are calculated with the sigma and epsilon. But I need to write this one with the C6 and C12 structure. If someone knows how to transform correctly this data, I’ll be really grateful.