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

[Justin Lemkul]

On 5/22/19 4:14 PM, Lalehan Ozalp wrote:
> 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
>

This entry cannot be correct, because the same atoms are defined in 
multiple ways. Note that the .hdb file requires atom *names*, not types. 
The errors listed below indicated you have 30 more hydrogens that are 
unaccounted for. FAD is a big molecule, you have to include all the 
hydrogens in the isoalloxazine, adenosine, and ribitol.

-Justin

> 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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================