GROMACS version: 2022
GROMACS modification: No
Hello!
I am trying to build a topology that includes a protein, water, ions, and a custom urea molecule with parameters specified in an itp file that I #included in forcefield.itp. pdb2gmx builts topol.top just fine, but when I try to grompp it, it complains that one of the urea atom types is missing, even though the itp file with the atom is included AND I have added the urea atoms to the atomtypes.atp file and I have added the atom types to the aminoacids.rtp file. I am using AMBER ff14sb_OL15 for the protein and TIP3P water. If I try to #include the urea itp file before including the rest of the stuff in the forcefield.itp file, it complains that the [ molecule type ] directive is out of order. I’m not sure how to resolve this problem. Please help! The urea itp file is below just in case, and it comes from the Smith group via Joan-Emma Shea’s group (in the SI of a paper).
Thank you,
Dan
; .itp file for Urea Smith
[ moleculetype ]
; Name nrexcl
UR 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CUR 1 UR C 1 0.921 12.0107
2 OUR 1 UR O 1 -0.675 15.99940
3 NUR 1 UR N1 1 -0.693 14.0067
4 HUR 1 UR H1 1 0.285 1.008
5 HUR 1 UR H2 1 0.285 1.008
6 NUR 1 UR N2 1 -0.693 14.0067
7 HUR 1 UR H3 1 0.285 1.008
8 HUR 1 UR H4 1 0.285 1.008
[ bonds ]
; ai aj funct b0 kb
1 2 1 0.1265 1.3100e+07
1 3 1 0.135 1.0300e+07
1 6 1 0.135 1.0300e+07
3 4 1 0.100 1.8700e+07
3 5 1 0.100 1.8700e+07
6 7 1 0.100 1.8700e+07
6 8 1 0.100 1.8700e+07
[ angles ]
; ai aj ak funct theta kb
1 3 4 1 120.0 390.0
1 3 5 1 120.0 390.0
1 6 7 1 120.0 390.0
1 6 8 1 120.0 390.0
4 3 5 1 120.0 445.0
7 6 8 1 120.0 445.0
3 1 6 1 117.2 670.0
2 1 3 1 121.4 730.0
2 1 6 1 121.4 730.0
[ dihedrals ]
; ai aj ak al funct phi cp mult
2 1 3 4 1 180.0 33.5 2
2 1 3 5 1 180.0 33.5 2
2 1 6 7 1 180.0 33.5 2
2 1 6 8 1 180.0 33.5 2
4 3 1 6 1 180.0 33.5 2
5 3 1 6 1 180.0 33.5 2
7 6 1 3 1 180.0 33.5 2
8 6 1 3 1 180.0 33.5 2
[ dihedrals ]
; ai aj ak al funct phi cp mult
3 4 5 1 2 0.0 167.4
6 7 8 1 2 0.0 167.4
1 3 6 2 2 0.0 167.4