<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. 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>
<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>
<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>
<p style="margin-bottom: 0in;">Sincerely,</p>
<p style="margin-bottom: 0in;">Yulian Gavrilov
</p></div>