[gmx-users] Question about adding hydrogens to a newly constructed residue
J. Nathan Scott
scottjn at chemistry.montana.edu
Mon Sep 5 17:44:04 CEST 2011
On Mon, Sep 5, 2011 at 9:29 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> On 6/09/2011 1:22 AM, J. Nathan Scott wrote:
>
>
>
> 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!
>
>
> Weird. Does naming the residue something other than CH6 help? Specifically,
> something all letters. Has that residue been added as Protein to the
> residuetypes.dat? General advice here:
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> Mark
>
Aha! That did the trick! I changed the residue name to CHB in the input PDB
file, the hdb file, the rtp file, and residuetypes.dat (I did have CH6
defined there as protein, by the way), and now pdb2gmx is adding those three
hydrogens with no problem whatsoever. Thank you again very much, it never
occurred to me that the residue name could be an issue.
I think I'll file a bug report on this. If nothing else this behavior is
certainly unexpected, since pdb2gmx never mentions any possible issues with
a number in the residue name.
Thank you again very much for your help with this!
-Nathan
--
----------
J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University
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