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

[J. Nathan Scott]

On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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.
>
> Mark
>

Hello Mark, thank you for your help, but I took your very reasonable advice
and am still receiving the exact same sort of error. I changed the PDB file
atom name to CQ, which of course makes it unique within that residue (and
indeed in the whole PDB file). I updated my .rtp entries and the .hdb rules
accordingly, and yet I still receive the exact same sort of error. It seems
as if something is wrong with my hdb syntax, but having looked at numerous
other examples in the hdb file and online I am at a loss as to what the
problem might be. For what it's worth, if I use the -missing switch when I
run pdb2gmx, the other CH6 hydrogen atoms appear to be added correctly in
the resulting gro file, with the names exactly as I expected from the hdb
naming rules.


My input:
pdb2gmx -f 2H5Q_spdbv.pdb -o 2H5Q_processed.gro -water tip3

Error received:
"WARNING: atom HQ1 is missing in residue CH6 66 in the pdb file
         You might need to add atom HQ1 to the hydrogen database of building
block CH6
         in the file aminoacids.hdb (see the manual)"

"WARNING: atom HQ2 is missing in residue CH6 66 in the pdb file
         You might need to add atom HQ1 to the hydrogen database of building
block CH6
         in the file aminoacids.hdb (see the manual)"

"WARNING: atom HQ3 is missing in residue CH6 66 in the pdb file
         You might need to add atom HQ1 to the hydrogen database of building
block CH6
         in the file aminoacids.hdb (see the manual)"



PDB file:
ATOM    493  CQ  CH6 A  66      42.848  20.230   6.798  1.00 40.19

hdb file:
CH6     9
2       6       HG1     CG1     SD      CB1
2       6       HB1     CB1     CG1     CA1
2       6       HA3     CA3     C3      N3
1       1       HB2     CB2     CA2     CG2
1       1       HD1     CD1     CE1     CG2
1       1       HD2     CD2     CE2     CG2
1       1       HE1     CE1     CD1     CZ
1       1       HE2     CE2     CD2     CZ
3       4       HQ      CQ      SD      CG1

rtp file (relevant portions only):
    CQ    opls_209      0.0     10
   HQ1    opls_140      0.0     11
   HQ2    opls_140      0.0     12
   HQ3    opls_140      0.0     13
[bonds]
    SD     CQ
    CQ   HQ1
    CQ   HQ2
    CQ   HQ3

I forgot to mention before, my GMX version is 4.5.4, running on a RHEL6
workstation. Thank you sincerely for any troubleshooting assistance you can
provide. I am quite stumped by this problem!

-Nathan

-- 
J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University
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