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<p style="margin-bottom: 0in;">Dear gmx users,</p>
<p style="margin-bottom: 0in;">I am trying to make a new isopeptide
bond between Lys and Gly in VERSION 4.5.4. I did it in VERSION 4.0.5
but can not do it in this version of Gromacs (steps are the same).</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;"><b>In PDB:</b></p><p style="margin-bottom: 0in;">...</p>
<p style="margin-bottom: 0in;">ATOM 1474 NZ LYN A 93 0.422
60.111 0.829 1.00 1.85 A N
</p>
<p style="margin-bottom: 0in;">...</p>
<p style="margin-bottom: 0in;">ATOM 1485 HZ1 LYN A 93 0.848
60.489 1.646 1.00 0.22 A H
</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">(only one HZ)</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">Terminal GLY also can be involved to
isopeptide bond:</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">ATOM 3827 N GLY B 240 2.191
62.558 -0.381 1.00 1.85 B N
</p>
<p style="margin-bottom: 0in;">ATOM 3828 CA GLY B 240 0.775
62.390 -0.063 1.00 2.17 B C
</p>
<p style="margin-bottom: 0in;">ATOM 3829 C GLY B 240 0.323
60.961 -0.200 1.00 2.00 B C
</p>
<p style="margin-bottom: 0in;">ATOM 3830 O GLY B 240 -0.097
60.559 -1.281 1.00 1.70 B O
</p>
<p style="margin-bottom: 0in;">ATOM 3831 HN GLY B 240 2.551
62.033 -1.148 1.00 0.22 B H
</p>
<p style="margin-bottom: 0in;">ATOM 3832 HA1 GLY B 240 0.209
62.976 -0.771 1.00 1.32 B H
</p>
<p style="margin-bottom: 0in;">ATOM 3833 HA2 GLY B 240 0.599
62.684 0.961 1.00 1.32 B H
</p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;">In Pymol the is a connection (NZ of
LYS93_domain_A – 0.13 nm – C of GLY240_domain_B).</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;"><b>I added: </b>
</p>
<p style="margin-bottom: 0in;"><b>1) </b>to ffbonded.itp</p>
<p style="margin-bottom: 0in;">[ angletypes ]</p>
<p style="margin-bottom: 0in;"></p>
<p style="margin-bottom: 0in;">HP CT N 1 109.500
418.400
</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">[ bondtypes ] etc. for ineptitude bond
are already exist</p>
<p style="margin-bottom: 0in;"><b>2) </b>to specbond.dat</p>
<p style="margin-bottom: 0in;">LYS NZ 1 GLY C
1 0.13 LYQ GLQ</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">GLQ the same as GLY (originally it
should be CGLY, it is C-terminal)</p>
<p style="margin-bottom: 0in;">LYQ the same as LYN, but only with one
HZ1 and [NZ N - 0.64977 17]
(instead of NZ N3)</p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;"><b>3) </b>Added LYQ and GLQ to the residuetype.dat
(to aminoacids.dat in VERSION 4.0.5)</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;"><b>4) </b>Added to aminoacids.hdb:</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">LYQ 7
</p>
<p style="margin-bottom: 0in;">1 1 H N -C CA
</p>
<p style="margin-bottom: 0in;">1 5 HA CA N CB C
</p>
<p style="margin-bottom: 0in;">2 6 HB CB CA CG
</p>
<p style="margin-bottom: 0in;">2 6 HG CG CB CD
</p>
<p style="margin-bottom: 0in;">2 6 HD CD CG CE
</p>
<p style="margin-bottom: 0in;">2 6 HE CE CD NZ
</p>
<p style="margin-bottom: 0in;">1 1 HZ NZ CE CD </p>
<p style="margin-bottom: 0in;">GLQ – same as GLY</p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;"><b>After</b></p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">pdb2gmx -f ubc7_94_t48_newgmx1.pdb -o
processed.gro -water tip3p -chainsep interactive -ignh -rtpres</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">There are no LYQ and GLQ topol.top
(instead of it LYS with 3 HZ3 and CGLY) and no bond (residues are not
connected after minimization).</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">Force field:</p>
<p style="margin-bottom: 0in;">AMBER99SB-ILDN force field
(Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
</p>
<p style="margin-bottom: 0in;">___________________________________<br>
</p>
<p style="margin-bottom: 0in;">In VERSION 4.0.5 first I changed names
of residues according to Amber (Amber 99) specificity:</p>
<p style="margin-bottom: 0in;">LYS to LYP and LYN etc.</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">And in specbond.dat it was:</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">LYN NZ 1 GLY C
1 0.13 LYQ GLQ (it works ok)<br></p>-- <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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