Ok… So I can just add the parameters in the ffbonded.itp and ffnonbonded.itp?
I tried adding the parameters in the corresponding files and ran the pdb2gmx command but only 4 atoms were present in the final gro file and all other atoms (from the original silica slab) were removed. What was more annoying was that those 4 atoms were not connected by any bonds. All I got was 4 atoms isolated in space.
Here I am attaching the files I added in the forcefield files:
1)Added in the .rtp file:
[ SIL ]
[ atoms ]
; name type charge chargegroup
SI SI 1.020 0
OW OW -0.510 1
H H 0.255 0
O O -0.993 1
[ bonds ]
; atom1 atom2 c0 c1
SI OW 0.1720 2.7042e+06
O H 0.0938 2.9551e+07
SI O 0.1690 1.9257e+06
[ angles ]
; atom1 atom2 atom3 th0 cth
SI O SI 166.00 64885.36
SI OW H 119.00 2211.40
O SI O 180.00 500.00
OW SI O 109.50 450.00
[ dihedrals ]
; atom1 atom2 atom3 atom4 phi0 cp mult
H OW SI O 180.00 1.00 3
O SI O SI 0.00 1.05 3
-
Added in the ffnonbonded.itp file:
SI 14 0.000 0.000 A 5.803853e-03 5.35358e-06
O 8 0.000 0.000 A 2.24192e-03 1.36137e-06
OW 8 0.000 0.000 A 2.24192e-03 1.36137e-06 -
the final gro file that I got:
3D Atomistic
4
1SIL SI 1 2.169 7.014 -0.182
1SIL OW 2 6.337 -0.752 -0.456
1SIL H 3 0.494 5.754 -0.455
1SIL O 4 2.952 -1.104 -0.091
5.84310 8.11840 0.36460
I am attaching all these for your reference. The pdb file I am attaching with this message (CONVERTED TO .dat format)topol.top (2.4 KB)
silica_slab_edited_OW.dat (718.4 KB)