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On 13/03/2011 9:53 PM, Yulian Gavrilov wrote:
<blockquote
cite="mid:AANLkTi=Of3DfrKHmXKi0cA8Rw1_u-HAWtc9T_zHjMrYL@mail.gmail.com"
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<p style="margin-bottom: 0in;">Thank you!</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">I use the correct “O” in Gly
according to .rtp and I checked it with vmd. There is really a
new
isopeptide bond. When there is no bond, after minimization and
equilibration, Gly and Lys just close to each other but they
are not
connected (in vmd). In my case they are connected (in vmd,
pymol). </p>
</div>
</blockquote>
<br>
None of these visualization programs read the topology in your .top
file. They just make guesses based on the geometry of the atoms in
the coordinate file. Anything you see that it guessed is irrelevant.
Read your pdb2gmx output, and go and look at the topology to see
what atoms have made a bond.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTi=Of3DfrKHmXKi0cA8Rw1_u-HAWtc9T_zHjMrYL@mail.gmail.com"
type="cite">
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<p style="margin-bottom: 0in;">When I look on step...pdb, one
these
residues is exploded (it's atoms are far from each other
outside of
the water box).</p>
<br>
<br>
<div class="gmail_quote">2011/3/13 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><br>
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;">
<div text="#000000" bgcolor="#ffffff">
<div class="im"> On 13/03/2011 8:55 PM, Yulian Gavrilov
wrote:
<blockquote type="cite">
<div dir="ltr">
<p style="margin-bottom: 0in;">Dear gmx users,</p>
<p style="margin-bottom: 0in;">I just started with
gromacs.</p>
<p style="margin-bottom: 0in;"> Can you help me to
find my mistake? I already asked about it, but I
did not understand what to do exactly in my case.</p>
<p style="margin-bottom: 0in;">I try to run to add a
new <b>isopeptide bone</b> to connect Lys and Gly
(to make a tetramer of <b>ubiquitin</b>).
I use AMBER99 force field, Gromacs 4.0.5.</p>
<p style="margin-bottom: 0in;">What I did:</p>
<ol>
<li>
<p style="margin-bottom: 0in;">I changed names
of residues according to AMBER rules (LYS to
LYN etc.). </p>
</li>
<li>
<p style="margin-bottom: 0in;">Added new type of
residues to ffamber.rtp (LYN -> LYQ and GLY
-> GLQ that are making a new isopeptide
bond) and added a new line to specbond.dat
(LYN NZ 1 GLY C 1 0.13 LYQ GLQ) to make such a
bond.</p>
</li>
</ol>
</div>
</blockquote>
<br>
</div>
IIRC, this creates a bond between the lysine side-chain
amine N and glycine *backbone* carbonyl C. You must use
the atom name for the side-chain carbonyl carbon (see .rtp
entry for GLY). If you've done this wrong, then specbond
will probably not have made a bond, because the backbone
carbonyl C was too far away. You should check your pdb2gmx
output carefully.
<div class="im"><br>
<br>
<blockquote type="cite">
<div dir="ltr">
<ol>
<li> <br>
</li>
<li>
<p style="margin-bottom: 0in;">Added new bond
type, angle type and dihedral type to
ffamber99bon.itp</p>
</li>
</ol>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;">After running of MD
(I've got good minimization and equilibration –
nvt and npt) I've got such an error:</p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">starting mdrun
'Protein in water'</font></p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">600000 steps,
1200.0 ps.</font></p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">step 94100,
will finish Sun Mar 13 08:15:56 2011</font></p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">Step 94124,
time 188.248 (ps) LINCS WARNING</font></p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">relative
constraint deviation after LINCS:</font></p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">rms 0.000796,
max 0.032792 (between atoms 2454 and 2456)</font></p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">bonds that
rotated more than 30 degrees:</font></p>
<p style="margin-bottom: 0in;"> <font
style="font-size: 9pt;" size="2">atom 1 atom 2
angle previous, current, constraint length</font></p>
<p style="margin-bottom: 0in;"> <font
style="font-size: 9pt;" size="2">2454 2457 35.6
0.1522 0.1545 0.1522</font></p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">And after it
the same type of errors with another atoms:</font></p>
<p style="margin-bottom: 0in;"> <font
style="font-size: 9pt;" size="2">2454 2456 36.1
0.1106 0.1113 0.1090 <font size="3">--> <b>Gly
CA and HA1, HA2</b></font></font></p>
<p style="margin-bottom: 0in;"> <font
style="font-size: 9pt;" size="2">2454 2455 40.5
0.1114 0.1103 0.1090</font></p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">.....</font></p>
<p style="margin-bottom: 0in;"> </p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">2454 2456 90.0
0.1078 0.1479 0.1090</font></p>
<p style="margin-bottom: 0in;"> <font
style="font-size: 9pt;" size="2">771 773 48.5
0.1011 0.1012 0.1010</font></p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">......</font></p>
<p style="margin-bottom: 0in;"> <font
style="font-size: 9pt;" size="2">771 773 39.8
0.1012 0.1005 0.1010 -<font size="3">-> <b>Gly
NZ and HZ1, HZ2</b></font></font></p>
<p style="margin-bottom: 0in;"> <font
style="font-size: 9pt;" size="2">771 772 34.9
0.1012 0.1030 0.1010</font></p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">....... </font>
</p>
<p style="margin-bottom: 0in;"><font
style="font-size: 9pt;" size="2">2454 2457 102.1
0.1490 38312886396780544.0000 0.1522</font></p>
<p style="margin-bottom: 0in;"> <font
style="font-size: 9pt;" size="2">2454 2456 83.0
5.9313 39290317874135040.0000 0.1090</font></p>
<p style="margin-bottom: 0in;">.......</p>
<p style="margin-bottom: 0in;">First errors are with
atoms from the residues with <b>new isopeptide
bond</b>. I suppose, that this bond is not good.</p>
</div>
</blockquote>
<br>
</div>
Seems like a reasonable hypothesis - but do look at 2454
and 2456 as well. You have to get out your trajectory and
a visualization package and see what is actually going
wrong. The warnings can be symptomatic of a problem that
started elsewhere.<br>
<br>
You say you've added new interaction types, but I see no
reason why you would need to. It's chemically so similar
to a backbone peptide that you may as well keep things the
same and model it the same way. Regardless, you should
probably check that the specbond.dat mechanism has created
interactions that make sense. Compare with a normal
peptide bond.<br>
<font color="#888888"> <br>
Mark</font>
<div class="im"><br>
<br>
<blockquote type="cite">
<div dir="ltr">
<p style="margin-bottom: 0in;">Please can you advice
me how yo make this isopeptide bond good?</p>
<p style="margin-bottom: 0in;">Can I just remove
this hydrogens?</p>
<br>
-- <br>
<div dir="ltr">
<p style="margin-bottom: 0in;">Sincerely,</p>
<p style="margin-bottom: 0in;">Yulian Gavrilov </p>
</div>
<br>
</div>
</blockquote>
<br>
</div>
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<br>
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<br>
<br clear="all">
<br>
-- <br>
<div dir="ltr">
<p style="margin-bottom: 0in;">
Sincerely,</p>
<p style="margin-bottom: 0in;">Yulian Gavrilov </p>
</div>
<br>
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