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    On 11/08/2011 7:24 PM, shahid nayeem wrote:
    <blockquote
cite="mid:CAB_3DJbc_jx-pWm18A95vL-drA3GhxTTLLtikywfT-qb0CCRsg@mail.gmail.com"
      type="cite">Hi Justin
      <div>I prepared a box of SOL and arginine Hydrochloride. But when
        I solvate my protein with this box now the positively charged
        arginine is as solvent and this causes problem in grompp. It
        gives error like "No such Molecule types ARG" etc. Solvating
        arginine with water and preparing a box was without error. which
        forcefield in gromacs has inbuilt .itp file for free amino acid
        which I can include in my .top file.</div>
    </blockquote>
    <br>
    See <a
      href="http://www.gromacs.org/Documentation/How-tos/Multiple_Chains">http://www.gromacs.org/Documentation/How-tos/Multiple_Chains</a>.
    Pre-position the non-water molecules, use pdb2gmx, solvate.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAB_3DJbc_jx-pWm18A95vL-drA3GhxTTLLtikywfT-qb0CCRsg@mail.gmail.com"
      type="cite">
      <div>Shahid Nayeem<br>
        <br>
        <div class="gmail_quote">On Fri, Jul 29, 2011 at 5:02 PM, Justin
          A. Lemkul <span dir="ltr">&lt;<a moz-do-not-send="true"
              href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex;">
            <div class="im"><br>
              <br>
              shahid nayeem wrote:<br>
              <blockquote class="gmail_quote" style="margin:0 0 0
                .8ex;border-left:1px #ccc solid;padding-left:1ex">
                Dear All I am trying to find the topology and
                parameterof free Arginine Hydrchloride molecule in
                gromacs force-field format. Developing it in Pro-Drg
                will not serve as &nbsp;I will need some other
                parametrization tool to check it charges. If someone can
                help, I will be grateful.<br>
              </blockquote>
              <br>
            </div>
            Isn't this just a protonated arginine (normal state for
            neutral pH) with a chloride counterion? &nbsp;There's nothing
            special about it, just run a coordinate file through pdb2gmx
            with the force field of your choice.<br>
            <br>
            -Justin<br>
            <br>
            -- <br>
            ========================================<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 moz-do-not-send="true" href="http://vt.edu"
              target="_blank">vt.edu</a> | (540) 231-9080<br>
            <a moz-do-not-send="true"
              href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
              target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
            <br>
            ========================================<br>
            <font color="#888888">
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