GROMACS version:
GROMACS modification: Yes/No
Here post your question
Fatal error:
Atom -C not found in residue ALY 14, rtp entry ALY while adding hydrogens
HETATM 2331 N ALY B 14 5.996 8.257 8.141 1.00 50.83
HETATM 2332 CA ALY B 14 4.967 8.879 9.032 1.00 50.81
HETATM 2333 C ALY B 14 4.026 7.800 9.485 1.00 51.13
HETATM 2334 O ALY B 14 4.055 7.388 10.640 1.00 52.80
HETATM 2335 CE ALY B 14 2.627 12.147 7.364 1.00 45.11
HETATM 2336 CD ALY B 14 3.231 11.178 6.354 1.00 46.03
HETATM 2337 CG ALY B 14 4.435 10.469 6.983 1.00 47.32
HETATM 2338 CB ALY B 14 4.115 9.991 8.407 1.00 48.29
HETATM 2339 CH ALY B 14 0.304 12.830 7.309 1.00 45.97
HETATM 2340 OH ALY B 14 -0.053 11.871 7.965 1.00 49.15
HETATM 2341 CH3 ALY B 14 -0.698 13.833 6.869 1.00 46.21
HETATM 2342 NZ ALY B 14 1.570 13.040 6.941 1.00 46.04
How to solve this problem?o(╥﹏╥)o I am going crazy…
ALY is not a standard residue, did you add it to your residue library & .hdb file? If so, mind sharing the respective entries?
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I hope I am making a contribution to this thread.
In CHARMM36 for example, there are entries for Acetylated lysine.
In charmm36_ljpme-jul2022.ff/aminoacids.rtp there is this entry
[ ALY ]
; acetylated Lysine
[ atoms ]
N NH1 -0.4700 1
HN H 0.3100 1
CA CT1 0.0700 1
HA HB1 0.0900 1
CB CT2 -0.1800 2
HB1 HA2 0.0900 2
HB2 HA2 0.0900 2
CG CT2 -0.1800 3
HG1 HA2 0.0900 3
HG2 HA2 0.0900 3
CD CT2 -0.1800 4
HD1 HA2 0.0900 4
HD2 HA2 0.0900 4
CE CT2 -0.0200 5
HE1 HA2 0.0900 5
HE2 HA2 0.0900 5
NZ NH1 -0.4700 5
HZ1 H 0.3100 5
CH C 0.5100 6
OH O -0.5100 6
CH3 CT3 -0.2700 7
HH31 HA3 0.0900 7
HH32 HA3 0.0900 7
HH33 HA3 0.0900 7
C C 0.5100 8
O O -0.5100 8
[ bonds ]
CB CA
CG CB
CD CG
CE CD
NZ CE
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
CD HD1
CD HD2
CE HE1
CE HE2
O C
NZ HZ1
NZ CH
CH OH
CH CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CA HN
C CA +N O
NZ CH CE HZ1
CH CH3 NZ OH
[ cmap ]
-C N CA C +N
and in charmm36_ljpme-jul2022.ff/aminoacids.hdb there is this one
ALY 8
1 1 HN N CA -C
1 5 HA CA C CB N
2 6 HB CB CA CG
2 6 HG CG CB CD
2 6 HD CD CE CG
2 6 HE CE CD NZ
1 1 HZ1 NZ CE CH
3 4 HH3 CH3 CH NZ
I hope this helps.
Ivan
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Thanks Ivan. Should I change the file? What should I do? Sorry that I know little about this field.o(╯□╰)o
How to add it to my residue library & .hdb file? I know little about that.o(╥﹏╥)o
Thanks @ivangreg, that’s helpful! I can imagine ALY is not recognized as a protein → it’s not treated by pdb2gmx as part of the polymer → the -C entry is not recognized as the carbonyl of the previous amino acid → the line in the .hdb cannot be processed.
The solution seems to be simple, copy residuetypes.dat to your local directory and before re-running pdb2gmx, add a line like:
ALY Protein
Let me know if that fixes it - I’m assuming ALY is already in your .hdb and .rtp as otherwise Gromacs would print a different error.
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Where would residuetypes.dat be located?
Depending on your installation, for me it’s in /usr/share/gromacs/top/.
On Unix check the location of your Gromacs executable with which gmx, typically it will be that folder + ../share/gromacs/top
Thank you.
I can confirm that, as @milosz.wieczor pointed out, the file is located here
/usr/local/gromacs/share/gromacs/top/residuetypes.dat
in an installation of GROMACS 2024.1
I can also confirm that in my installation /residuetypes.dat did not have an entry for ALY.
So, probably, adding it as suggested could be a solution.
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Hi @ZhangYi .
Did the solution proposed by @milosz.wieczor work?
It would be nice to leave a note of success/failure for the next person finding the same error.
Thank you
Ivan
Yes! It worked!I have solved this problem. Thank you very much!