GROMACS version: 2022.4
GROMACS modification: No
I am trying to implement an adenylylated (AMPylated) tyrosine residue as additional entry in “aminoacids.rtp” of the charmm36-jul2022 forcefield. I obtained a stream-file (.str) from CGenFF for the modified residue, which I converted to .itp and .prm using “cgenff_charmm2gmx.py”. After creating the corresponding .rtp entry for my modified residue, I can run pdb2gmx without problems but grompp gives errors related to “No default Bond types”, “No default U-B types” and “No default Proper Dih. types”, which does not get resolved with adding the parameter file inclusion statement “#include yam.prm” to topol.top. I am not sure if this is related to the atom types I am using, since I did not rename the CGenFF atom types in my rtp file entry? Although all the atom types I am using are listed in “atomtypes.atp”, I am not sure if there is a full set of parameters for all CGenFF atom types in my rtp file entry?
Here would be my rtp file entry for the modified (i.e. AMPylated) tyrosine residue:
[ YAM ]
;
[ atoms ]
N NH1 -0.4700 1
H07 H 0.3100 1
CA CT1 0.0700 1
H08 HB1 0.0900 1
CB CT2 -0.1800 2
CG CA 0.0000 3
CD1 CA -0.1150 4
CD2 CA -0.1150 4
CE1 CA -0.1150 5
CE2 CA -0.1150 5
CZ CA 0.1100 6
OH OH1 -0.2380 6
P PG1 1.4030 7
O2P OG2P1 -0.7210 7
O3P OG2P1 -0.7210 7
C5' CG321 -0.0730 8
O5' OG303 -0.5820 8
C4' CG3C51 0.1310 9
O4' OG3C51 -0.4620 9
C3' CG3C51 0.1420 10
O3' OG311 -0.6470 10
C2' CG3C51 0.1410 11
O2' OG311 -0.6480 11
C1' CG3C51 0.1440 12
N1 NG2R62 -0.7410 13
C2 CG2R64 0.4950 14
N3 NG2R62 -0.7510 15
C4 CG2RC0 0.4260 16
C5 CG2RC0 0.2800 17
C6 CG2R64 0.4630 18
N6 NG2S3 -0.7640 19
N7 NG2R50 -0.7180 20
C8 CG2R53 0.3390 21
N9 NG2R51 -0.0560 22
H09 HGR62 0.1280 23
H02 HGR52 0.1410 24
H012 HGR61 0.1150 25
H014 HGR61 0.1150 26
H05 HGR61 0.1150 27
H06 HGR61 0.1150 28
H11 HGA2 0.0900 30
H12 HGA2 0.0900 31
H14 HGA2 0.0900 32
H15 HGA2 0.0900 33
H16 HGA1 0.0900 34
H17 HGA1 0.0900 35
H18 HGP1 0.4200 36
H19 HGA1 0.0900 37
H20 HGP1 0.4200 38
H21 HGA1 0.0900 39
H22 HGP4 0.3770 40
H23 HGP4 0.3770 41
C C 0.5100 42
O O -0.5100 42
[ bonds ]
N CA
N H07
CA C
CA CB
CA H08
C O
CB CG
CB H11
CB H12
CG CD1
CG CD2
CD1 CE1
CD1 H014
CD2 CE2
CD2 H06
CE1 CZ
CE1 H012
CE2 CZ
CE2 H05
CZ OH
OH P
P O2P
P O3P
P O5'
C5' O5'
C5' C4'
C5' H14
C5' H15
C4' O4'
C4' C3'
C4' H16
O4' C1'
C3' O3'
C3' C2'
C3' H17
O3' H18
C2' O2'
C2' C1'
C2' H19
O2' H20
C1' H21
N1 C2
N1 C6
C2 N3
C2 H09
N3 C4
C4 C5
C5 C6
C5 C8
C6 N6
N6 H22
N6 H23
N7 C5
N7 C8
N9 C1'
N9 C8
N9 C4
[ impropers ]
N -C CA H07
C CA +N O
[ cmap ]
-C N CA C +N
I would be very happy for any help to resolve this issue.
Many thanks
Michael