Hi there,<div><br></div><div>Since ILDN dihedrals has some parameters with up to periodicity 6, I was wondering if it's possible to convert it in RB with 6 coefficients. If so, what would be the formula? For example, for converting the usual Amber99SB to RB I have:</div>
<div><br></div><div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">if</span> phase <span style="color: #2157f9">in</span> [<span style="color: #1b49da">0</span>, <span style="color: #1b49da">180</span>]:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">if</span> kPhi > <span style="color: #1b49da">0</span>: V[period] = <span style="color: #1b49da">2</span> * kPhi * cal</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">if</span> period == <span style="color: #1b49da">1</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">0</span>] += <span style="color: #1b49da">0.5</span> * V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">if</span> phase == <span style="color: #1b49da">0</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">1</span>] -= <span style="color: #1b49da">0.5</span> * V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">else</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">1</span>] += <span style="color: #1b49da">0.5</span> * V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">elif</span> period == <span style="color: #1b49da">2</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">if</span> phase == <span style="color: #1b49da">180</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">0</span>] += V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">2</span>] -= V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">else</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">2</span>] += V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">elif</span> period == <span style="color: #1b49da">3</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">0</span>] += <span style="color: #1b49da">0.5</span> * V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">if</span> phase == <span style="color: #1b49da">0</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">1</span>] += <span style="color: #1b49da">1.5</span> * V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">3</span>] -= <span style="color: #1b49da">2</span> * V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">else</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">1</span>] -= <span style="color: #1b49da">1.5</span> * V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">3</span>] += <span style="color: #1b49da">2</span> * V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">elif</span> period == <span style="color: #1b49da">4</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">if</span> phase == <span style="color: #1b49da">180</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">2</span>] += <span style="color: #1b49da">4</span> * V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">4</span>] -= <span style="color: #1b49da">4</span> * V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> <span style="color: #2157f9">else</span>:</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">0</span>] += V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">2</span>] -= <span style="color: #1b49da">4</span> * V[period]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"> C[<span style="color: #1b49da">4</span>] += <span style="color: #1b49da">4</span> * V[period]</p><div><br></div>So, as you can see, I can handle up to 4 periods (C[5] is always 0, but not with ILDN and I need to add C[6] rules as well).</div>
<div><br></div><div>Any ideas? Many thanks in advance,</div><div><br></div><div>Alan<br>-- <br>Alan Wilter SOUSA da SILVA, DSc<div>Bioinformatician, UniProt - PANDA, EMBL-EBI<br>CB10 1SD, Hinxton, Cambridge, UK</div><div>
+44 1223 49 4588</div><br>
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