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

J. Nathan Scott scottjn at chemistry.montana.edu
Sun Sep 4 19:30:43 CEST 2011

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
   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!


J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110904/95478913/attachment.html>

More information about the gromacs.org_gmx-users mailing list