GROMACS version:
GROMACS modification: Yes/No
Hi.
I have obtained topology files using Cgenff and ATB, and there is a significant difference between the two files.
In the topology file of the gromos54a7 force field obtained with ATB, the items such as [ bonds ], [ angles ], etc. have lengths, angles, and energy… values as shown below.
[ bonds ]
; ai aj funct c0 c1
1 2 2 0.0971 7.9547e+06
2 3 2 0.1380 1.1000e+07
3 4 2 0.1400 8.5400e+06
3 11 2 0.1400 8.5400e+06
4 5 2 0.1090 1.2300e+07
…
[ angles ]
; ai aj ak funct angle fc
1 2 3 2 109.50 450.00
2 3 4 2 121.00 685.00
2 3 11 2 121.00 685.00
4 3 11 2 120.00 560.00
3 4 5 2 120.00 505.00
3 4 6 2 120.00 560.00
However, in the topology file of the charmm36 force field obtained with Cgenff (I used charmm-gui), there are no such values in those fields.
[ bonds ]
; ai aj funct b0 Kb
1 2 1
1 6 1
1 8 1
…
[ angles ]
; ai aj ak funct th0 cth S0 Kub
2 1 6 5
2 1 8 5
6 1 8 5
1 2 3 5
1 2 145 5
3 2 145 5
2 3 4 5
I know that ATB provides QM calculations within the site, unlike cgenff. only for atom index
Are those values omitted because they don’t have that much impact on the simulation? Or are they missing because the one generated by cgenff is not a QM calculation?(it generated the output in a few seconds…) I don’t know the reason for the difference between the two files.
Thank you.!!