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On 6/09/2011 1:44 AM, J. Nathan Scott wrote:
<blockquote
cite="mid:CAHktqcECjWdwef-3ii9caxXZxmuRqKOtPronFW_AQOn3EPa5ww@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On Mon, Sep 5, 2011 at 9:29 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
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<div bgcolor="#FFFFFF" text="#000000">
<div>
<div class="h5"> On 6/09/2011 1:22 AM, J. Nathan Scott
wrote:
<blockquote type="cite"><br>
<br>
<div class="gmail_quote">On Sun, Sep 4, 2011 at 11:51
AM, Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
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<div>
<div>On 5/09/2011 3:30 AM, J. Nathan Scott
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex"> Hello fellow
GROMACS users,<br>
<br>
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).<br>
<br>
Relevant RTP lines:<br>
CE3 opls_209 0.0 10<br>
HE31 opls_140 0.0 11<br>
HE32 opls_140 0.0 12<br>
HE33 opls_140 0.0 13<br>
CE1 opls_145 0.0 32<br>
HE1 opls_146 0.0 33<br>
CE2 opls_145 0.0 34<br>
HE2 opls_146 0.0 35<br>
[bonds]<br>
CE3 HE31<br>
CE3 HE32<br>
CE3 HE33<br>
CE1 HE1<br>
CE2 HE2<br>
<br>
Relevant HDB lines:<br>
3 4 HE3 CE3 SD CG1<br>
1 1 HE1 CE1 CD1 CZ<br>
1 1 HE2 CE2 CD2 CZ<br>
<br>
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):<br>
<br>
"WARNING: atom HE31 is missing in residue
CH6 66 in the pdb file<br>
You might need to add atom HE31 to
the hydrogen database of building block CH6<br>
in the file aminoacids.hdb (see the
manual)"<br>
<br>
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!<br>
</blockquote>
<br>
</div>
</div>
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.<br>
<br>
Mark<br>
</blockquote>
<div><br>
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.<br>
<br>
<br>
My input:<br>
pdb2gmx -f 2H5Q_spdbv.pdb -o 2H5Q_processed.gro
-water tip3<br>
<br>
Error received:<br>
"WARNING: atom HQ1 is missing in residue CH6 66 in
the pdb file<br>
You might need to add atom HQ1 to the
hydrogen database of building block CH6<br>
in the file aminoacids.hdb (see the
manual)"<br>
<br>
"WARNING: atom HQ2 is missing in residue CH6 66 in
the pdb file<br>
You might need to add atom HQ1 to the
hydrogen database of building block CH6<br>
in the file aminoacids.hdb (see the
manual)"<br>
<br>
"WARNING: atom HQ3 is missing in residue CH6 66 in
the pdb file<br>
You might need to add atom HQ1 to the
hydrogen database of building block CH6<br>
in the file aminoacids.hdb (see the
manual)"<br>
<br>
<br>
<br>
PDB file:<br>
ATOM 493 CQ CH6 A 66 42.848 20.230
6.798 1.00 40.19<br>
<br>
hdb file:<br>
CH6 9<br>
2 6 HG1 CG1 SD CB1<br>
2 6 HB1 CB1 CG1 CA1<br>
2 6 HA3 CA3 C3 N3<br>
1 1 HB2 CB2 CA2 CG2<br>
1 1 HD1 CD1 CE1 CG2<br>
1 1 HD2 CD2 CE2 CG2<br>
1 1 HE1 CE1 CD1 CZ<br>
1 1 HE2 CE2 CD2 CZ<br>
3 4 HQ CQ SD CG1<br>
<br>
rtp file (relevant portions only):<br>
CQ opls_209 0.0 10<br>
HQ1 opls_140 0.0 11<br>
HQ2 opls_140 0.0 12<br>
HQ3 opls_140 0.0 13<br>
[bonds]<br>
SD CQ<br>
CQ HQ1<br>
CQ HQ2<br>
CQ HQ3<br>
<br>
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!<br>
</div>
</div>
</blockquote>
<br>
</div>
</div>
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: <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><br>
<font color="#888888"> <br>
Mark<br>
</font></div>
</blockquote>
<div><br>
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.<br>
<br>
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.<br>
</div>
</div>
</blockquote>
<br>
Yes, please do that on the GROMACS Redmine. Please provide a tarball
of a set of files that can reproduce the issue.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAHktqcECjWdwef-3ii9caxXZxmuRqKOtPronFW_AQOn3EPa5ww@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div><br>
Thank you again very much for your help with this!<br>
<br>
-Nathan<br>
</div>
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<br>
-- <br>
----------<br>
J. Nathan Scott, Ph.D.<br>
Postdoctoral Fellow<br>
Department of Chemistry and Biochemistry<br>
Montana State University<br>
<br>
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