<div class="Section1">
<p class="MsoNormal">Dear All:</p>
<p class="MsoNormal"> How are you.</p>
<p class="MsoNormal" style="TEXT-INDENT: 9pt"><span> </span>Sorry to bother you. I am trying do use <span class="SpellE">gromacs</span><span> </span>to do MD on a protein-<span class="SpellE">ligand</span> complex. I am following Dr. Kerrigan's tutorial on simulation of protein-<span class="SpellE">ligand</span> complex. Here I have a question about the topology of <span class="SpellE">ligand</span> generated by <span class="SpellE">prodrg</span>. And when I run pdb2gmx on my protein(with gmx force field), I noticed <span class="SpellE">hydrogens</span> were added to <span class="SpellE">benzene</span> rings. But when I look at the itp file and pdb file with polar H generated by prodrg, I noticed there are no hydrogens added to benzene ring of my ligand. I am just wondering if this will affect the simulation, and what I should do. Thank you so much for your help.</p>
<p class="MsoNormal" style="TEXT-INDENT: 9pt"> </p>
<p class="MsoNormal" style="TEXT-INDENT: 9pt"> </p>
<p class="MsoNormal" style="TEXT-INDENT: 9pt"> </p>
<p class="MsoNormal" style="TEXT-INDENT: 9pt">Best Regards,</p>
<p class="MsoNormal" style="TEXT-INDENT: 9pt">mao</p></div>