[gmx-users] Question about adding hydrogens to a newly constructed residue

Mark Abraham Mark.Abraham at anu.edu.au
Sun Sep 4 19:51:31 CEST 2011

On 5/09/2011 3:30 AM, J. Nathan Scott wrote:
> Hello fellow GROMACS users,
> I am in the process of constructing a new residue in the OPLS-AA force 
> field for the mCherry chromophore. However, I am having some 
> difficulty in adding three CH3 hydrogens. In the 2H5Q PDB structure 
> the chromophore residue, CH6, has CE1 and CE2 ring carbons defined, 
> but also an extended chain carbon named CE. The problem is that my hdb 
> rules were assigning HE1 and HE2 to the ring carbon hydrogens (1       
> 1       HE1     CE1     CD1     CZ for example), and HE1, HE2, and HE3 
> to the CE carbon hydrogens (3       4       HE     CE     SD      
> CG1). Since these hydrogens are of different types, I need to have 
> them named distinctly in my RTP file and need for Gromacs to 
> understand them as different types. I changed the CH6 residue's CE 
> atom to CE3 in the PDB file and the relevant RTP entries accordingly 
> (see below). I also changed the hdb entry for the new CE3 atom (also 
> below).
> Relevant RTP lines:
>    CE3    opls_209      0.0     10
>   HE31    opls_140      0.0     11
>   HE32    opls_140      0.0     12
>   HE33    opls_140      0.0     13
>    CE1    opls_145      0.0     32
>    HE1    opls_146      0.0     33
>    CE2    opls_145      0.0     34
>    HE2    opls_146      0.0     35
>  [bonds]
>    CE3  HE31
>    CE3  HE32
>    CE3  HE33
>    CE1   HE1
>    CE2   HE2
> Relevant HDB lines:
> 3       4       HE3     CE3     SD      CG1
> 1       1       HE1     CE1     CD1     CZ
> 1       1       HE2     CE2     CD2     CZ
> I thought this would cover everything, but I am receiving the 
> following sort of error from pdb2gmx for each of the the three CE3 
> hydrogens(pdb2gmx -f 2H5Q.pdb -o 2H5Q_processed.gro -water tip3):
> "WARNING: atom HE31 is missing in residue CH6 66 in the pdb file
>          You might need to add atom HE31 to the hydrogen database of 
> building block CH6
>          in the file aminoacids.hdb (see the manual)"
> I've looked at other examples in the aminoacids.hdb file and cannot 
> figure out what I am missing here, it seems like my hdb rule should be 
> adding 3 type 4 hydrogens named HE31, HE32, and HE33. I am assuming 
> that the other hdb rules are OK, since they seemed to work fine 
> before, as indicated by examining the gro file. I would sincerely 
> appreciate any help you can offer. Thank you!

I can't see a reason why that wouldn't work. However, there's no need 
for you to preserve the PDB atom name for CE. Reducing the potential for 
some atom-naming screw-up such as this is a good reason to change it (in 
both your coordinate file and .rtp entry). It will probably just work, 
or at the very least simplify further trouble-shooting.


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