<br /><br /><span>On 03/01/11, <b class="name">zeppelin zeppelin </b> <zzeppelin87@gmail.com> wrote:</span><blockquote cite="mid:AANLkTikknemO0=_jOcBu4N4f4ASqZXh9=2fT1OQpHgo0@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div dir="ltr"><p style="margin-bottom: 0in;">Dear GROMACS users,</p>
<p style="margin-bottom: 0in;">I started to work with gromacs (version
4.0.5) only several weeks ago and I need your help.</p></div></div></blockquote><br />In that case, you'll be best served by starting with the most recent version of GROMACS, not one that's 3 years old. Force field organization has changed, and AMBER forcefields are fully integrated.<br /><br /><blockquote cite="mid:AANLkTikknemO0=_jOcBu4N4f4ASqZXh9=2fT1OQpHgo0@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div dir="ltr"><p style="margin-bottom: 0in;"> Now I am trying
to add a new <b>isopeptide bone</b> to connect Lys and Gly (to make a
dimer of <b>ubiquitin</b>). I use AMBER force field.
</p>
<p style="margin-bottom: 0in;">What I did:</p>
<p style="margin-bottom: 0in;">1. Added new type of residues to
ffamber.rtp</p>
<p style="margin-bottom: 0in;">LIQ – LYN that is close enough to GLY
(GLQ) to make an isopeptide bond. Distance – 0.13
</p>
<p style="margin-bottom: 0in;">2. I added this line to specbond.dat:
</p>
<p style="margin-bottom: 0in;">LYN NZ 1 GLY C
1 0.13 LYQ GLQ</p>
<p style="margin-bottom: 0in;">3. Added new bond type, angle type and
dihedral type to ffamber99bon.itp:</p></div></div></blockquote><br />Why do you think you need to do this? What's wrong with the existing atom and functional types? Use (for example) glutamide and backbone peptides as models for what you want to achieve.<br /><br /><blockquote cite="mid:AANLkTikknemO0=_jOcBu4N4f4ASqZXh9=2fT1OQpHgo0@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div dir="ltr"><p style="margin-bottom: 0in;"></p>
<p style="margin-bottom: 0in;">For example:</p>
<p style="margin-bottom: 0in;">[ angletypes ]</p>
<p style="margin-bottom: 0in;">; i j k func
th0 <b>cth</b></p>
<p style="margin-bottom: 0in;">HW OW HW 1 104.520
836.800 ; TIP3P water</p>
<p style="margin-bottom: 0in;">HW HW OW 1 127.740
0.000 ; (found in crystallographic water with 3 bonds)</p>
<p style="margin-bottom: 0in;">C C O 1
120.000 669.440 ; new99</p>
<p style="margin-bottom: 0in;">.........................................
</p>
<p style="margin-bottom: 0in;"><span style="font-weight: bold;">new lines</span>:</p>
<p style="margin-bottom: 0in;">C CT N3 1 110.100
527.184 ; FOR UBIQ YULIAN <span style="font-weight: bold;">line 344</span></p>
<p style="margin-bottom: 0in;">C N3 H 1 120.000
418.400 ; FOR UBIQ YULIAN</p>
<p style="margin-bottom: 0in;">N3 C O 1 122.900
669.440 ; FOR UBIQ YULIAN</p>
<p style="margin-bottom: 0in;">CT C N3 1 116.600
585.760 ; FOR UBIQ YULIAN</p>
<p style="margin-bottom: 0in;">C N3 CT 1 121.900
418.400 ; FOR UBIQ YULIAN</p>
<p style="margin-bottom: 0in;">C N3 H 1 120.000
418.400 ; FOR UBIQ YULIAN</p>
<p style="margin-bottom: 0in;"><br />
</p>
<p style="margin-bottom: 0in;">Here I added a new angle types just by
copying a close type of angle in simple peptide bone and changing N
to N3 (for isopeptide bone)</p></div></div></blockquote><br />But the nitrogen in an isopeptide bond is neutral. N should be fine. Why are you buying trouble?<br /><br /><blockquote cite="mid:AANLkTikknemO0=_jOcBu4N4f4ASqZXh9=2fT1OQpHgo0@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div dir="ltr"><p style="margin-bottom: 0in;"></p>
<p style="margin-bottom: 0in;">4. But in ffamber99.atp one can found
that these atoms are different (sp2 and sp3 type of hybridization):</p>
<p style="margin-bottom: 0in;">amber99_34 14.01000 N sp2
nitrogen in amide groups</p>
<p style="margin-bottom: 0in;">amber99_39 14.01000 N3 sp3 N
for charged amino groups (Lys, etc)</p>
<p style="margin-bottom: 0in;">5. I checked in PyMol the real value of
different angles in isopeptide bond and found, of course, that they
are differ from angles in simple peptide bond.
</p>
<p style="margin-bottom: 0in;">6. So when I change N to N3 I did not
get a real isippeptide bone. And my <b><u>question </u></b>is: How to
make a new isopeptide bone with correct value of angles and
dihedrals. I can simply change the value of angle (by measuring in
pymol), but I do not know what is <b><u>cth </u></b><span style=""><span style="text-decoration: none;">
in [ angletypes ] section of ffamber99bon.itp and how to change it
correctly.</span></span></p>
<p style="margin-bottom: 0in;">P. S. After this change I have such a
warning in gromacs runnings</p>
<p style="margin-bottom: 0in;">"WARNING 1 [file ffamber99bon.itp, <span style="font-weight: bold;">line
344</span>]:</p>
<p style="margin-bottom: 0in;"> Overriding Angle parameters.</p>
<p style="margin-bottom: 0in;"> old: 111.2 669.44 111.2 669.44
</p>
<p style="margin-bottom: 0in;"> new: C CT N3 1 110.100
527.184"</p>
<p style="margin-bottom: 0in;">What does it really mean (during
editing ffamber99bon.itp I just added several lines and did not
remove anything)?
</p></div></div></blockquote><br />It means that there was already an angle type for C-CT-N3 before you invented a new one, and GROMACS is warning you that one definition is replacing the other. It's up to you judge whether that is sensible.<br /><br />Mark