<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks Kass for the help.<br><br>I want to specifically protonate one of the lysine near the active site and deprotonate Tyr and Ser. It will be kind if you can please help me to know how to select that specific residue number.<br><br>Regards<br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Mon, 27/9/10, Itamar Kass <i><itamar.kass@monash.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Itamar Kass <itamar.kass@monash.edu><br>Subject: Re: [gmx-users] Query regarding protonation and deprotonation of some residues<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Monday, 27 September, 2010, 10:07 AM<br><br><div id="yiv956642841">
Hi,<br>
<br>
You need to define the protonation sate vie pdb2gmx.<br>
<br>
pdb2gmx -tyr -lys <br>
<br>
On 27/09/10 2:34 PM, sonali dhindwal wrote:
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<td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">Hello All,<br>
<br>
I came through this research article, in which author has
selectively deprotonated and protonated some of the
residues to
simulate the condition for electrostatic interaction with
the substrate while carrying out molecular dynamics
simulation.<br>
<br>
It will be appreciable, if
you could help me regarding the same, how to deprotonate
Tyr
and Ser residue and protonate Lysine residue of the
protein while
preparing the protein topology to be used for molecular
dynamics simulation in Gromacs.<br>
<br>
Thanks and Regards.<br>
<br>
<div>--<br>
Sonali Dhindwal</div>
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<pre class="yiv956642841moz-signature">-- <br><br><br>"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut<br><br>===========================================<br>| Itamar Kass, Ph.D.<br>| Postdoctoral Research Fellow<br>|<br>| Department of Biochemistry and Molecular Biology<br>| Building 77 Clayton Campus<br>| Wellington Road<br>| Monash University,<br>| Victoria 3800<br>| Australia<br>|<br>| Tel: +61 3 9902 9376<br>| Fax: +61 3 9902 9500<br>| E-mail: <a rel="nofollow" class="yiv956642841moz-txt-link-abbreviated" ymailto="mailto:Itamar.Kass@monash.edu" target="_blank" href="/mc/compose?to=Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a><br>============================================</pre>
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