On 6/09/2011 1:44 AM, J. Nathan Scott wrote:
On Mon, Sep 5, 2011 at 9:29 AM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@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.abra...@anu.edu.au <mailto:mark.abra...@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.
Yes, please do that on the GROMACS Redmine. Please provide a tarball of
a set of files that can reproduce the issue.
Mark
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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