[gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic

[Elisa Pieri]

Hello again,

we are trying to add Amber lipids to the Amber94 force field (actually, it
is a version where a few years ago we added a ligand). We used pdb2gmx as
"pdb2gmx -f file.pdb" and we successfully created a conf.gro and topol.top
file (and posre.itp and top.itp per lipid molecule). Then, when we tried to
used grompp as "grompp -f file.mdp -p topol.top -c conf.gro -o conf.tpr",
we got many warnings of the type

This is an example of the warnings:
WARNING 15 [file ffnonbonded.itp, line 78]: Too few parameters on line
(source file /home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
line 338)

And a fatal error:
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
line: 742
Fatal error: Unknown bond_atomtype hE

I'm showing you what additions we made (in particular, for hE).
We added the new atomtypes (20) in the atomtypes.atp file in the form:
hE                 1.00800      ; lipid H bonded to aliphatic carbon with 1
electron withdrawing group

Then we added the parameters in the ffbonded.itp file; example of
stretching, bendind and torsions for hE:

cA hE         1    0.10930   281081.1 ; lipid

cA cA hE             1   110.070    387.940
cB cA hE             1   110.460    393.547
hE cA hE             1   109.550    327.858
hE cA nN             1   109.500    416.559
hE cA oH             1   109.880    426.517
hE cA oS             1   108.820    425.429
hE cA oT             1   109.500    418.400

cA  cA  cA  hE    9       0.0      0.65103     3
cB  cB  cA  hE    9       0.0      0.00000     2
cC  cA  cA  hE    9       0.0      0.65103     3
cC  nN  cA  hE    9       0.0      0.00000     2
cC  oS  cA  hE    9       0.0      1.60373     3
hA  cA  cA  hE    9       0.0      0.65103     3
hB  cB  cA  hE    9       0.0      0.00000     2
hE  cA  cA  hE    9       0.0      0.65103     3
hE  cA  cA  hX    9       0.0      0.65103     3
hE  cA  cA  nA    9       0.0      0.65103     3
hE  cA  cA  nN    9       0.0      0.65084     3
hE  cA  cA  oH    9       0.0      0.00000     3
hE  cA  cA  oH    9       0.0      1.04600     1
hE  cA  cA  oS    9       0.0      0.00000     3
hE  cA  cA  oS    9       0.0      1.04600     1
hE  cA  cA  oT    9       0.0      0.00000     3
hE  cA  cA  oT    9       0.0      1.04600     1
hE  cA  nN  hN    9       0.0      0.00000     2
hE  cA  oH  hO    9       0.0      2.09200     3
hE  cA  oT  pA    9       0.0      1.60387     3

Same thing for the ffnonbonded.itp:
hE           1       1.008   0.0000  A   2,47135e-01  6,56888e-02

And then we created a lipids.rtp file (here an example for a PC part of a
lipid):
[ PC ]
 [ atoms ]
   C11    cC           0.798859              1
   O12    oC          -0.627537              2
   O11    oS          -0.424905              3
   C1     cA          -0.002091              4
   HR     hE           0.119283              5
   HS     hE           0.119283              6
   C2     cA           0.081076              7
   HX     hE           0.131246              8
   C3     cA           0.095565              9
   HA     hE           0.069089             10
   HB     hE           0.069089             11
   O31    oZ          -0.445682             12
   P31    pA           1.076564             13
   O32    oZ          -0.445682             14
   C31    cA           0.363063             15
   H1A    hE           0.013458             16
   H1B    hE           0.013458             17
   C32    cA          -0.282326             18
   H2A    hX           0.164858             19
   H2B    hX           0.164858             20
   N31    nA           0.198554             21
   C33    cA          -0.395982             22
   H3A    hX           0.194775             23
   H3B    hX           0.194775             24
   H3C    hX           0.194775             25
   C34    cA          -0.395982             26
   H4A    hX           0.194775             27
   H4B    hX           0.194775             28
   H4C    hX           0.194775             29
   C35    cA          -0.395982             30
   H5A    hX           0.194775             31
   H5B    hX           0.194775             32
   H5C    hX           0.194775             33
   O33    oP          -0.793092             34
   O34    oP          -0.793092             35
   O21    oS          -0.390929             36
   C21    cC           0.787558             37
   O22    oC          -0.625551             38
 [ bonds ]
    C11   O12
    C11   O11
    O11   C1
    C1    HR
    C1    HS
    C1    C2
    C2    HX
    C2    C3
    C2    O21
    C3    HA
    C3    HB
    C3    O31
    O31   P31
    P31   O32
    P31   033
    P31   034
    O32   C31
    C31   H1A
    C31   H1B
    C31   C32
    C32   H2A
    C32   H2B
    C32   N31
    N31   C33
    N31   C34
    N31   C35
    C33   H3A
    C33   H3B
    C33   H3C
    C34   H4A
    C34   H4B
    C34   H4C
    C35   H5A
    C35   H5B
    C35   H5C
    O21   C21
    C21   022

Can you spot the mistake(s)?

Thank you very much for your help in advance,
Elisa