Dear Abdul,<br><br>I had a similar error always with residue number 2 when using the amber ports in gromacs. Manually adding the hydrogen to the backbone nitrogen that connects to residue 1 will fix this.<br><br>You might know how to do this but just in case here is how I do it:<br>
<br>load your pdb into any builder and add the hydrogen into a reasonable position(i.e no steric clash) on the nitrogen. write out a pdb. I find that builders can change the format of pdb's so I usually just copy the H line and add it into my original pdb formatting it as needed. <br>
<br>It is the only H that needs to be defined. pdb2gmx will take care of the rest.<br><br>I'm not sure why this happens but I didn't look too much into it at the time as I was learning how to use gromacs and everything was going wrong :) <br>
<br>Hope this helps,<br><br>Oliver<br><br><div class="gmail_quote">On 3 July 2010 16:50, Carsten Kutzner <span dir="ltr"><<a href="mailto:ckutzne@gwdg.de">ckutzne@gwdg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div style="word-wrap: break-word;">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><blockquote type="cite"><div style="margin: 0px;"><span style="font-family: 'Helvetica'; font-size: medium;"><b>From: </b></span><span style="font-family: 'Helvetica'; font-size: medium;">"abdul wadood" <<a href="mailto:wadoodbiochemist@hotmail.com" target="_blank">wadoodbiochemist@hotmail.com</a>><br>
</span></div><div style="margin: 0px;"><span style="font-family: 'Helvetica'; font-size: medium;"><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: 0px;"><span style="font-family: 'Helvetica'; font-size: medium;"><b>To: </b></span><span style="font-family: 'Helvetica'; font-size: medium;"><<a href="mailto:ckutzne@gwdg.de" target="_blank">ckutzne@gwdg.de</a>><br>
</span></div><div style="margin: 0px;"><span style="font-family: 'Helvetica'; font-size: medium;"><b>Subject: </b></span><span style="font-family: 'Helvetica'; font-size: medium;"><b>missing atom</b><br></span></div>
<br><span style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: medium;"><div 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> </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> </span><br>Research Scholar,<span> </span><br>
Dr.Panjwani Center for Molecular Medicine and<span> </span><br>Drug Research,<span> </span><br>International Center for Chemical and<span> </span><br>Biological Science,<span> </span><br>University of Karachi, Karachi-75720, Pakistan.<span> </span><br>
Email:<a href="mailto:wadoodbiochemist@hotmail.com" target="_blank">wadoodbiochemist@hotmail.com</a><span> </span><br></div><br><br></div></span></blockquote></div><div><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; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><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; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><br>
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<br></div></div><br>--<br>
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