Edit your pdb as per ur rtp file / forcefield.<br><br>
<div><span class="gmail_quote">On 16/06/2009, <b class="gmail_sendername">Justin A. Lemkul</b> <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span class="q"><br><br>nitu sharma wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear all,<br><br> i am trying to simulation of dna-protein complex using gromacs with amber port . I am using amber99 port with gromacs-4.0.3 version. I am facing problem in running pdb2gmx command .The error comes like this-<br>
-------------------------------------------------------<br>Program pdb2gmx, VERSION 4.0.3<br>Source code file: resall.c, line: 426<br><br>Fatal error:<br>Residue 'T' not found in residue topology database<br><br>Can anyone suggest me how can I overcome this problem .<br>
<br></blockquote><br></span><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://oldwiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database" target="_blank">http://oldwiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database</a><br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span class="q">Thanks a lot in advance.<br><br>Nitu sharma<br>Jawaherlal Nehru University<br><br><br></span>------------------------------------------------------------------------<br>
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========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
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