Segmentation fault when gmx pdb2gmx

GROMACS version:2021.03
GROMACS modification: No
Dear Gromacs users,
I’ve mutated a DC to 5MC in a single DNA chain,and arranged to run MD simulation in amber99sb forcefield.As a preparation,I add 5MC in residuetypes.dat,I also appended 5MC forcefields to dna.rtp and hydrogen to dna.hdb,such as:

[ 5MC ]
 [ atoms ]
     P    P             1.16590     1
   O1P    O2           -0.77610     2
   O2P    O2           -0.77610     3
   O5'    OS           -0.49540     4
   C5'    CT           -0.00690     5
  H5'1    H1            0.07540     6
  H5'2    H1            0.07540     7
   C4'    CT            0.16290     8
   H4'    H1            0.11760     9
   O4'    OS           -0.36910    10
   C1'    CT           -0.01160    11
   H1'    H2            0.19630    12
    N1    N*           -0.03890    13
    C6    CM           -0.14850    14
    H6    H4            0.27290    15
    C5    CM           -0.19270    16
    C7    CT           -0.27790    17
   H71    HC            0.09430    18
   H72    HC            0.09430    19
   H73    HC            0.09430    20
    C4    CA            0.79940    21
    N4    N2           -0.95710    22
   H41    H             0.41630    23
   H42    H             0.41630    24
    N3    NC           -0.77500    25
    C2    C             0.74010    26
    O2    O            -0.60090    27
   C3'    CT            0.07130    28
   H3'    H1            0.09850    29
   C2'    CT           -0.08540    30
  H2'1    HC            0.07180    31
  H2'2    HC            0.07180    32
   O3'    OS           -0.52320    33
 [ bonds ]
     P   O1P
     P   O2P
     P   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N1
   C1'   C2'
    N1    C6
    N1    C2
    C6    H6
    C6    C5
    C5    C7
    C5    C4
    C7   H71
    C7   H72
    C7   H73
    C4    N4
    C4    N3
    N4   H41
    N4   H42
    N3    C2
    C2    O2
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
  -O3'     P
 [ impropers ]
    C2    C6    N1   C1'
    N1    N3    C2    O2 
    C4   H41    N4   H42
    N1    C5    C6    H6
    C6    C4    C5    H5
    C5    N4    C4    N3
    C4    C6    C5    C7

However,when I began to run pdb2gmx,it’s suddenly break down and show Segmentation fault.Is there any typing error or something ? I cant help this awkward situation.

You should never get a segmentation fault, even with incorrect input.

Can you check if pdb2gmx works correctly with these 5MC entries in the force field, but with an input that doesn’t use 5MC?

Thanks for reply!
I’ve tried with the input that doesn’t use 5MC,it could work out successfully.But when it happens to the structure with 5MC,it turns to be a fatal error .It works like:

Checking for duplicate atoms....

Generating any missing hydrogen atoms and/or adding termini.
Segmentation fault

I guess it’s about dna.hdb

Could you file an issue on gitlab here:

and attach all input files need to run grompp? You will need an account.

If that’s too complicated for you, I can also do it, but then I will need all input files.