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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><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>
<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>
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