GROMACS version: 2023.1
GROMACS modification: Yes/No
Here post your question:
I struggle with the following error: “Fatal error:
Residue ‘GDP’ not found in residue topology database”. The same error occurs for GTP.
This is despite having added the parameters for GDP and GTP in my aminoacids.rtp file (or rna.rtp), in my atomtypes.atp and my ffnonbonded.itp in the same format as the files already has.
I’ve also included these lines in residuetypes.dat: " GDP Other
GTP Other".
Appreciate all the help I can get to solve this issue!
Here is how I’ve added information in my files.
aminoacids.rtp:
"[ GTP ]
[ atoms ]
O1G O3 -0.9526 1
PG P 1.265 2
O2G O3 -0.9526 3
O3G O3 -0.9526 4
O3B OS -0.5322 5
PB P 1.3852 6
O1B O2 -0.8894 7
O2B O2 -0.8894 8
O3A OS -0.5689 9
PA P 1.2532 10
O1A O2 -0.8799 11
O2A O2 -0.8799 12
O5’ OS -0.5987 13
C5’ CT 0.0558 14
H5’1 H1 0.0679 15
H5’2 H1 0.0679 16
C4’ CT 0.1065 17
H4’ H1 0.1174 18
O4’ OS -0.3548 19
C1’ CT 0.0191 20
H1’ H2 0.2006 21
N9 N* 0.0492 22
C8 CK 0.1374 23
H8 H5 0.164 24
N7 NB -0.5709 25
C5 CB 0.1744 26
C6 C 0.477 27
O6 O -0.5597 28
N1 NA -0.4787 29
H1 H 0.3424 30
C2 CA 0.7657 31
N2 N2 -0.9672 32
H21 H 0.4364 33
H22 H 0.4364 34
N3 NC -0.6323 35
C4 CB 0.1222 36
C3’ CT 0.2022 37
O3’ OH -0.6541 38
H3T HO 0.4376 39
H3’ H1 0.0615 40
C2’ CT 0.067 41
H2’1 H1 0.0972 42
O2’ OH -0.6139 43
HO’2 HO 0.4186 44
[ bonds ]
O1G PG
PG O2G
PG O3G
PG O3B
O3B PB
PB O1B
PB O2B
PB O3A
O3A PA
PA O1A
PA O2A
PA O5’
O5’ C5’
C5’ H5’1
C5’ H5’2
C5’ C4’
C4’ H4’
C4’ O4’
O4’ C1’
C1’ H1’
C1’ N9
N9 C8
C8 H8
C8 N7
N7 C5
C5 C6
C6 O6
C6 N1
N1 H1
N1 C2
C2 N2
N2 H21
N2 H22
C2 N3
N3 C4
C4 C3’
C3’ O3’
O3’ H3T
C3’ H3’
C3’ C2’
C2’ H2’1
C2’ O2’
O2’ HO’2
[ impropers ]
C8 C4 N9 C1’
C5 N1 C6 O6
C6 C2 N1 H1
C2 H21 N2 H22
N7 N9 C8 H8
N1 N3 C2 N2
[ LOOP CLOSING EXPLICIT ]
C1’ C2’
C4 C5
C4 N9"
atomtypes.atp:
; GTP-specific atom types
PG 30.97000 ; phosphate in GTP
PB 30.97000 ; phosphate in GTP
PA 30.97000 ; phosphate in GTP
O1G 16.00000 ; phosphate oxygen in GTP
O2G 16.00000 ; phosphate oxygen in GTP
O3G 16.00000 ; phosphate oxygen in GTP
O3B 16.00000 ; phosphate oxygen in GTP
O1B 16.00000 ; phosphate oxygen in GTP
O2B 16.00000 ; phosphate oxygen in GTP
O3A 16.00000 ; phosphate oxygen in GTP
O1A 16.00000 ; phosphate oxygen in GTP
O2A 16.00000 ; phosphate oxygen in GTP
O5’ 16.00000 ; ribose oxygen in GTP
ffnonbonded.itp:
“; GTP-specific atom types
PG 15 30.97 0.0000 A 3.74177e-01 8.36800e-01 ; Phosphate phosphorus
PB 15 30.97 0.0000 A 3.74177e-01 8.36800e-01 ; Phosphate phosphorus
PA 15 30.97 0.0000 A 3.74177e-01 8.36800e-01 ; Phosphate phosphorus
O1G 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; Phosphate oxygen
O2G 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; Phosphate oxygen
O3G 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; Phosphate oxygen
O3B 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; Phosphate oxygen
O1B 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; Phosphate oxygen
O2B 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; Phosphate oxygen
O3A 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; Phosphate oxygen
O1A 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; Phosphate oxygen
O2A 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; Phosphate oxygen
O5’ 8 16.00 0.0000 A 3.06647e-01 8.80314e-01 ; Ribose oxygen”