Segmentation fault when gmx pdb2gmx

User discussions
1

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.
Regards,
Loong

2

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?

3

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

4

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.