On 6/09/2011 1:22 AM, J. Nathan Scott wrote:
On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham <[email protected]
<mailto:[email protected]>> 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
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