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Hi, <div><br></div><div>I'm trying to create virtual atoms for the hydrogens in a glycosylated protein, specifically the hydrogens on the sugar. I have three types of hydrogens bound to carbon: CH on ring carbon, CH2 on branched carbon, CH3 methyl group. I also have OH and NH hydrogens.</div><div><br></div><div>Three questions:</div><div><br></div><div>1. Should all of these be 4fd type hydrogens because they are all ~sp3 hybridized geometry around the carbon (puckered ring, branched, methyl)?</div><div><br></div><div>2. I understand that I'll have to add a line like the following for each of my virtual atoms. Can somebody please clarify what function 1 is, and what the a,b and d parameters are? </div><div><br></div><div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Helvetica">[ virtual sites4 ]</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Helvetica">; Site from funct a b d</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Helvetica">5 1 2 3 4 1 0.33333 0.33333 -0.105</p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Helvetica"><br></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Helvetica"><span class="Apple-style-span" style="font-family: Verdana; font-size: 13px;">3. What is the best way to handle the OH and NH hydrogens?</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Helvetica"><span class="Apple-style-span" style="font-family: Verdana; font-size: 13px;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Helvetica"><span class="Apple-style-span" style="font-family: Verdana; font-size: 13px;">Thank you for any advice!</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Helvetica"><span class="Apple-style-span" style="font-family: Verdana; font-size: 13px;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Helvetica"><span class="Apple-style-span" style="font-family: Verdana; font-size: 13px;">Relly</span></p></div><br /><hr />Express your personality in color! Preview and select themes for Hotmail®. <a href='http://www.windowslive-hotmail.com/LearnMore/personalize.aspx?ocid=TXT_MSGTX_WL_HM_express_032009#colortheme' target='_new'>See how.</a></body>
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