[gmx-users] error of missing atoms due to an incorrectness in the .hdb file

[Lalehan Ozalp]

Hello all,

I am trying to run a simulation with a protein involving a covalently bound
FAD cofactor. I followed the steps provided on the website
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
and -I think- added the hydrogens in the .hdb file accordingly. While doing
this, I specifically used the atom types that gromacs would recognize (I
also added relevant .rtp and .itp file to the forcefield in the current
working directory).

However, several warnings and subsequently a fatal error occurs when I run
pdb2gmx. I don't prefer using -missing option in this case as it'll
probably give a wrong topology.

How to come around this? Any help would be appreciated. I provide the
warnings and the error message below; as well as the constitution of the
hydrogens in the .hdb file:
(.hdb file)
FAD 6
2 3 H N2    CA  NC
3 4 HC CT CA CA
1      1      HC CA CA CT
1 1 H5 CQ NC CA
1 1 H5 CQ NA CT
1 1 HA CA CA CT


WARNING: atom H01 is missing in residue FAD 600 in the pdb file
         You might need to add atom H01 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H02 is missing in residue FAD 600 in the pdb file
         You might need to add atom H02 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H03 is missing in residue FAD 600 in the pdb file
         You might need to add atom H03 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H04H is missing in residue FAD 600 in the pdb file
         You might need to add atom H04H to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H05 is missing in residue FAD 600 in the pdb file
         You might need to add atom H05 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H06H is missing in residue FAD 600 in the pdb file
         You might need to add atom H06H to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H07 is missing in residue FAD 600 in the pdb file
         You might need to add atom H07 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H08H is missing in residue FAD 600 in the pdb file
         You might need to add atom H08H to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H09 is missing in residue FAD 600 in the pdb file
         You might need to add atom H09 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H10 is missing in residue FAD 600 in the pdb file
         You might need to add atom H10 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H11 is missing in residue FAD 600 in the pdb file
         You might need to add atom H11 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H12 is missing in residue FAD 600 in the pdb file
         You might need to add atom H12 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H13 is missing in residue FAD 600 in the pdb file
         You might need to add atom H13 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H14 is missing in residue FAD 600 in the pdb file
         You might need to add atom H14 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H15 is missing in residue FAD 600 in the pdb file
         You might need to add atom H15 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H16 is missing in residue FAD 600 in the pdb file
         You might need to add atom H16 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H17 is missing in residue FAD 600 in the pdb file
         You might need to add atom H17 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H18 is missing in residue FAD 600 in the pdb file
         You might need to add atom H18 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H19 is missing in residue FAD 600 in the pdb file
         You might need to add atom H19 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H21 is missing in residue FAD 600 in the pdb file
         You might need to add atom H21 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H22 is missing in residue FAD 600 in the pdb file
         You might need to add atom H22 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H23 is missing in residue FAD 600 in the pdb file
         You might need to add atom H23 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H24 is missing in residue FAD 600 in the pdb file
         You might need to add atom H24 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H25 is missing in residue FAD 600 in the pdb file
         You might need to add atom H25 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H26 is missing in residue FAD 600 in the pdb file
         You might need to add atom H26 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H27 is missing in residue FAD 600 in the pdb file
         You might need to add atom H27 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H29 is missing in residue FAD 600 in the pdb file
         You might need to add atom H29 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H30 is missing in residue FAD 600 in the pdb file
         You might need to add atom H30 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H31 is missing in residue FAD 600 in the pdb file
         You might need to add atom H31 to the hydrogen database of
building block FAD
         in the file FAD.hdb (see the manual)


WARNING: atom H4 is missing in residue FAD 600 in the pdb file
         You might need to add atom H4 to the hydrogen database of building
block FAD
         in the file FAD.hdb (see the manual)


-------------------------------------------------------
Program:     gmx pdb2gmx, version 2016.4
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1584)

Fatal error:
There were 30 missing atoms in molecule Non-Protein_chain_A2, if you want to
use this incomplete topology anyhow, use the option -missing

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors