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On 13/03/2011 8:55 PM, Yulian Gavrilov wrote:
<blockquote
cite="mid:AANLkTinoRxxtteLMpz0MndGxHq4CvodTvsnju+9ZVB1_@mail.gmail.com"
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<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>
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.<br>
<br>
<blockquote
cite="mid:AANLkTinoRxxtteLMpz0MndGxHq4CvodTvsnju+9ZVB1_@mail.gmail.com"
type="cite">
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<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>
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>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTinoRxxtteLMpz0MndGxHq4CvodTvsnju+9ZVB1_@mail.gmail.com"
type="cite">
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<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>
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