Dangling bond error with capped phosphorylated amino acid

User discussions
1

GROMACS version: 2019.3
GROMACS modification: No

I have a capped phosphoserine (ACE-SP2-NME) that I have modified through Pymol from a capped serine (ACE-SER-NME).
I am trying to use force field ff03ws from Best et al. and using the .rtp files for SEP2 from SwissSideChain.
The PDB looks like this:

> Blockquote
ATOM      1  C   ACE     1       1.673  -0.297  -0.088  1.00  0.00           C
ATOM      2  O   ACE     1       2.204  -1.252  -0.688  1.00  0.00           O
ATOM      3  CH3 ACE     1       0.171  -0.293   0.109  1.00  0.00           C
ATOM      4 1HH3 ACE     1      -0.101  -1.004   0.875  1.00  0.00           H
ATOM      5 2HH3 ACE     1      -0.163   0.687   0.410  1.00  0.00           H
ATOM      6 3HH3 ACE     1      -0.323  -0.562  -0.813  1.00  0.00           H
ATOM      7  N   SP2     2       2.366   0.680   0.385  1.00  0.00           N
ATOM      8  CA  SP2     2       3.672   1.062  -0.169  1.00  0.00           C
ATOM      9  C   SP2     2       4.297   2.166   0.654  1.00  0.00           C
ATOM     10  O   SP2     2       3.614   3.013   1.230  1.00  0.00           O
ATOM     11  CB  SP2     2       3.611   1.467  -1.673  1.00  0.00           C
ATOM     12  OG  SP2     2       2.971   2.663  -1.963  1.00  0.00           O
ATOM     13  P01 SP2     2       1.634   3.009  -1.749  0.00  0.00           P
ATOM     14  O01 SP2     2       1.189   4.233  -2.526  0.00  0.00           O
ATOM     15  O02 SP2     2       0.859   1.804  -2.531  0.00  0.00           O
ATOM     16  O03 SP2     2       1.128   2.855  -0.329  0.00  0.00           O
ATOM     17  H   SP2     2       1.972   1.234   1.141  1.00  0.00           H
ATOM     18  HA  SP2     2       4.335   0.182  -0.082  1.00  0.00           H
ATOM     19 2HB  SP2     2       3.192   0.635  -2.267  1.00  0.00           H
ATOM     20 3HB  SP2     2       4.659   1.589  -2.046  1.00  0.00           H
ATOM     21  N   NME     3       5.580   2.213   0.761  1.00  0.00           N
ATOM     22  CH3 NME     3       6.203   3.187   1.640  1.00  0.00           C
ATOM     23  H   NME     3       6.155   1.569   0.237  1.00  0.00           H
ATOM     24 1HH3 NME     3       5.976   4.188   1.306  1.00  0.00           H
ATOM     25 2HH3 NME     3       5.838   3.062   2.650  1.00  0.00           H
ATOM     26 3HH3 NME     3       7.276   3.053   1.638  1.00  0.00           H
CONECT    1    2    3    7
CONECT    2    1
CONECT    3    1    4    5    6
CONECT    4    3
CONECT    5    3
CONECT    6    3
CONECT    7    1    8   17
CONECT    8    7    9   11   18
CONECT    9    8   10   21
CONECT   10    9
CONECT   11    8   12   19   20
CONECT   12   11   13
CONECT   13   12   15   16   14
CONECT   14   13
CONECT   15   13
CONECT   16   13
CONECT   17    7
CONECT   18    8
CONECT   19   11
CONECT   20   11
CONECT   21    9   22   23
CONECT   22   21   24   25   26
CONECT   23   21
CONECT   24   22

When I run pdb2gmx, it seems that GROMACS is reading only the ACE cap and SP2, but not NME. I get the following error:
chain #res #atoms
1 ’ ’ 2 13
2 ’ ’ 1 2

WARNING: there were 4 atoms with zero occupancy and 0 atoms with
occupancy unequal to one (out of 15 atoms). Check your pdb file.

Opening force field file ./amber03ws_withSEP.ff/atomtypes.atp
Atomtype 70
Reading residue database… (Amber03ws_withSEP)
Opening force field file ./amber03ws_withSEP.ff/aminoacids.rtp
Residue 131
Sorting it all out…
Opening force field file ./amber03ws_withSEP.ff/dna.rtp
Residue 147
Sorting it all out…
Opening force field file ./amber03ws_withSEP.ff/rna.rtp
Residue 163
Sorting it all out…
Opening force field file ./amber03ws_withSEP.ff/aminoacids.hdb
Opening force field file ./amber03ws_withSEP.ff/dna.hdb
Opening force field file ./amber03ws_withSEP.ff/rna.hdb
Opening force field file ./amber03ws_withSEP.ff/aminoacids.n.tdb
Opening force field file ./amber03ws_withSEP.ff/aminoacids.c.tdb
Processing chain 1 (13 atoms, 2 residues)
Identified residue ACE1 as a starting terminus.
Identified residue SP22 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

Program: gmx pdb2gmx, version 2019.3
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1062)

Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal residues
so that they match the residue database (.rtp) entries, or provide terminal
database entries (.tdb).

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

Where in the PDB file could the problem be? Or is it the .rtp parameters?

Thank you

Best,

Anne

2

Hi Anne,

Prior to any technical comments, the .rtp files you linked seem to be meant for a CHARMM FF, judging from the atom types and the presence of CMAPs - not sure if they will work well with ff03ws (which is an Amber family FF).

Then, as pdb2gmx notes, your atoms 13-16 have an occupancy of 0.00 (9th column in the PDB file you pasted), that’s likely the reason they are ignored.

Best,
Miłosz

3

This is suggestive of the issue. SP2 is identified as the last residue instead of NME. Can you please share the entire command and full output from the terminal? There is often subtle diagnostic information that is very useful when troubleshooting pdb2gmx issues.