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
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