<div>Thank you Justin. According to pKalfa values at pH=7 HIS has q=+36e. In this case is it better to treat as noncharged or positively charged (+1) as we perform simulation at pH=7 ? How would you treat it?</div>
<div> </div>
<div>Steven<br><br></div>
<div class="gmail_quote">On Tue, Feb 28, 2012 at 4:02 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="im"><br><br>Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Dear Gmx Users,<br> Does anyone know why in Charmm27 ff under Gromacs the residue HIS is taken as residue HSE from rtp file and written as NONcharged?<br>
<br></blockquote><br></div>pdb2gmx decides the protonation state to assign based on a hydrogen bond network search. This is true for all force fields. If you are unsatisfied with the chosen protonation, there are command line options to interactively change the protonation state of any titratable residues.<br>
<br>-Justin<br><br>-- <br>==============================<u></u>==========<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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