<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Abdul,<div><br></div><div>please keep all Gromacs-related questions on the mailing list.</div><div><br></div><div>Best,</div><div> Carsten</div><div><br></div><div><br></div><div><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">"abdul wadood" <<a href="mailto:wadoodbiochemist@hotmail.com">wadoodbiochemist@hotmail.com</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">July 3, 2010 8:40:29 AM GMT+02:00<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><<a href="mailto:ckutzne@gwdg.de">ckutzne@gwdg.de</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>missing atom</b><br></span></div><br><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">Dear Carsten<br><br>I am running simulation using gromacs with amber forcefields on my protein. I have prepared the input file accordingly and have all the required library. But the problem is that when i run pdb2gmx for the top file the following error come:<br><br>WARNING: atom H is missing in residue LEU 2 in the pdb file<br> You might need to add atom H to the hydrogen database of residue LEU<br> in the file ff???.hdb<span class="Apple-converted-space"> </span><br><br>I tried my best to solve the problem, searching on the gromacs website and manual but cannot succeed.<br>If you kindly help me in this respect your help will be highly appreciated by our group our research.<br>the input file is attached.<br><br>Many regards<br><br><div>Abdul Wadood,<span class="Apple-converted-space"> </span><br>Research Scholar,<span class="Apple-converted-space"> </span><br>Dr.Panjwani Center for Molecular Medicine and<span class="Apple-converted-space"> </span><br>Drug Research,<span class="Apple-converted-space"> </span><br>International Center for Chemical and<span class="Apple-converted-space"> </span><br>Biological Science,<span class="Apple-converted-space"> </span><br>University of Karachi, Karachi-75720, Pakistan.<span class="Apple-converted-space"> </span><br>Email:<a href="mailto:wadoodbiochemist@hotmail.com">wadoodbiochemist@hotmail.com</a><span class="Apple-converted-space"> </span><br></div><br><br></div></span></blockquote></div><div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></span>
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