GROMACS version:
GROMACS modification: Yes/No
Dear Gromacs users,
I am trying to obtain the topology for a protein that includes a non-standard residue (LLP). I have modified the aminoacids.rtp, aminoacids.hdb, atomtypes.atp, ffnonbonded, and ffbonded files for amber03 (attached). However, I continue to encounter an error when I run the command: gmx_mpi pdb2gmx -f AMX_start.pdb -o 1AMX_processed.gro -ter -ignh which I report below:
"Generating any missing hydrogen atoms and/or adding termini.
-------------------------------------------------------
Program: gmx pdb2gmx, version 2024.1
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 154)
Fatal error:
Residue 651 named LLP of a molecule in the input file was mapped
to an entry in the topology database, but the atom 5 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
For more information and tips for troubleshooting, please check the GROMACS
website at Common errors when using GROMACS - GROMACS 2024.2 documentation"
Please could you help me to solve such error?
Best,
Daniele Veclani.
Could you provide the [ atoms ] block of the rtp entry for LLP as well as the lines from the PDB file of that residue? There seems to be a mismatch in the atoms.
Yes sure,
This is the [Atom] of rtp file:
“[ LLP ]
[ atoms ]
N n8 -0.911800 1
CA c3 0.155500 2
CB c3 -0.117400 3
CG c3 -0.070400 4
CD c3 -0.117400 5
CE c3 0.138800 6
NZ n2 -0.655900 7
C4’ ce 0.467800 8
C4 ca -0.085900 9
C3 ca -0.000200 10
O oh -0.489100 11
C2 ca 0.283600 12
C2’ c3 -0.127400 13
C5 ca -0.125600 14
C6 ca 0.335200 15
N1 nb -0.680000 16
C5’ c3 0.234700 17
OP4 os -0.565200 18
P p5 1.320901 19
OP1 o -0.915500 20
OP2 o -0.915500 21
OP3 o -0.915500 22
C c 0.649100 23
O o -0.630000 24
H hn 0.401300 25
HA h1 0.053700 26
H10 hc 0.070200 27
H11 hc 0.070200 28
H12 hc 0.046200 29
H13 hc 0.046200 30
H14 hc 0.065200 31
H15 hc 0.065200 32
H16 h1 0.012200 33
H17 h1 0.012200 34
H18 h1 0.024200 35
H19 h1 0.024200 36
HZ h1 0.377500 37”
And here I report the pdb strucutres:
"ATOM 5276 N LLP A 651 11.104 13.207 0.654 1.00 0.00 N
ATOM 5277 CA LLP A 651 12.345 12.459 0.276 1.00 0.00 C
ATOM 5278 CB LLP A 651 12.655 12.876 -1.134 1.00 0.00 C
ATOM 5279 CG LLP A 651 13.465 11.876 -1.934 1.00 0.00 C
ATOM 5280 CD LLP A 651 13.865 12.276 -3.234 1.00 0.00 C
ATOM 5281 CE LLP A 651 14.265 11.276 -4.134 1.00 0.00 C
ATOM 5282 NZ LLP A 651 14.565 12.676 -5.134 1.00 0.00 N
ATOM 5283 C4’ LLP A 651 15.565 12.676 -6.134 1.00 0.00 C
ATOM 5284 C4 LLP A 651 16.565 12.676 -7.134 1.00 0.00 C
ATOM 5285 C3 LLP A 651 17.565 12.676 -8.134 1.00 0.00 C
ATOM 5286 O LLP A 651 18.565 12.676 -9.134 1.00 0.00 O
ATOM 5287 C2 LLP A 651 19.565 12.676 -10.134 1.00 0.00 C
ATOM 5288 C2’ LLP A 651 20.565 12.676 -11.134 1.00 0.00 C
ATOM 5289 C5 LLP A 651 21.565 12.676 -12.134 1.00 0.00 C
ATOM 5290 C6 LLP A 651 22.565 12.676 -13.134 1.00 0.00 C
ATOM 5291 N1 LLP A 651 23.565 12.676 -14.134 1.00 0.00 N
ATOM 5292 C5’ LLP A 651 24.565 12.676 -15.134 1.00 0.00 C
ATOM 5293 OP4 LLP A 651 25.565 12.676 -16.134 1.00 0.00 O
ATOM 5294 P LLP A 651 26.565 12.676 -17.134 1.00 0.00 P
ATOM 5295 OP1 LLP A 651 27.565 12.676 -18.134 1.00 0.00 O
ATOM 5296 OP2 LLP A 651 28.565 12.676 -19.134 1.00 0.00 O
ATOM 5297 OP3 LLP A 651 29.565 12.676 -20.134 1.00 0.00 O
ATOM 5298 C LLP A 651 30.565 12.676 -21.134 1.00 0.00 C
ATOM 5299 O LLP A 651 31.565 12.676 -22.134 1.00 0.00 O "
I checked for any inconsistencies between the two files, but everything seems to be correct (I believe).
Thank for your help.
Best,
Daniele.