<div>Dear all,</div><div><br></div><div>I am trying to run simulation with phosphorylated Threonine (TRO) and I found lot's of info about this issue reading previous posts which explained on how to patch the force-field files and define this modified amino acid. After looking at the community forcefield offered here <a href="http://www.gromacs.org/Downloads/User_contributions/Force_fields">http://www.gromacs.org/Downloads/User_contributions/Force_fields</a></div>
<div><br></div><div>After exploring those files what calls my attention is that in the *.hdb file that describes which atoms are protonated is seems to have an issue that I wanted to double-check with the rest of the members. It seems to me that the CH3 group is not protonated in the phosphotyrosine (TRO) as shown below</div>
<div><br></div><div><span style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)">Extracted from *.hdp file</span><br style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)">
<div style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)">THR 2 </div><div style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)">
1<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>H<span class="Apple-tab-span" style="white-space:pre"> </span>N<span class="Apple-tab-span" style="white-space:pre"> </span>-C<span class="Apple-tab-span" style="white-space:pre"> </span>CA</div>
<div style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)">1<span class="Apple-tab-span" style="white-space:pre"> </span>2<span class="Apple-tab-span" style="white-space:pre"> </span>HG1<span class="Apple-tab-span" style="white-space:pre"> </span>OG1<span class="Apple-tab-span" style="white-space:pre"> </span>CB<span class="Apple-tab-span" style="white-space:pre"> </span>CA</div>
<div style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)"><br></div><div style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)"><div>TPO 1</div>
<div>1 1 H N -C CA</div></div><div style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)">...but where is the 2nd line???</div><div style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)">
<br></div><div style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)">Why THR has 2 lines why the TRO having the PO3 group has only one line? Can somebody explain this?</div><div style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)">
<br></div><div style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)">Kirill</div><div style="font-family:'Times New Roman';font-size:16px;background-color:rgb(255,255,255)">
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