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On 13/03/2011 10:05 PM, Yulian Gavrilov wrote:
<blockquote
cite="mid:AANLkTi=4VX6J5LFpP4L74y7WykWidorhqtVzCDLGpTON@mail.gmail.com"
type="cite">
<div dir="ltr">Yes, I checked topol.top. There are all isopeptide
bonds ,that I want (according to atom contacts, angles, etc.)<br>
</div>
</blockquote>
<br>
Perhaps I've been labouring under a misapprehension. You've
mentioned an isopeptide bond, which usually happens between a
side-chain carboxylic acid (GLU,ASP) and a side-chain amino acid
(LYS), but also you've mentioned GLY, which only has a backbone
carbonyl. My brain read "GLY" as "GLU". I would not expect pdb2gmx
to cope correctly with terminating the glycine via specbond.dat.
Please show us the [atoms] and [bonds] section for LYQ and GLYQ in
your .top file.<br>
<br>
There were other points I made in an early email to which you've not
responded, also.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTi=4VX6J5LFpP4L74y7WykWidorhqtVzCDLGpTON@mail.gmail.com"
type="cite">
<div dir="ltr"><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 9:53 PM, Yulian Gavrilov
wrote:
<blockquote type="cite">
<div dir="ltr">
<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>
</div>
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>
<font color="#888888"> <br>
Mark</font>
<div>
<div class="h5"><br>
<br>
<blockquote type="cite">
<div dir="ltr">
<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"
target="_blank">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> 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><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><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>
</div>
<br>
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-- <br>
<div dir="ltr">
<p style="margin-bottom: 0in;"> Sincerely,</p>
<p style="margin-bottom: 0in;">Yulian Gavrilov </p>
</div>
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</blockquote>
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-- <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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</blockquote>
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