2009/11/17 Nilesh Dhumal <span dir="ltr"><<a href="mailto:ndhumal@andrew.cmu.edu">ndhumal@andrew.cmu.edu</a>></span><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
this is the command,<br>
<br>
pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter<br>
<br>
Here I have attached the dioxin.pdb file.<br></blockquote><div> </div><div>Check your dioxing.pdb.. there might be formatting issues. It might happen the due to bad format of the pdb file, your 'L' is somehow removed from 'CL'. Follow the file format on pdb's website [<a href="http://www.pdb.org/pdb/static.do?p=file_formats/index.jsp#pdb">http://www.pdb.org/pdb/static.do?p=file_formats/index.jsp#pdb</a>]<br>
<br>-Manik<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
IN di.pbd there is no CL atoms.<br>
<font color="#888888">NIlesh</font><br>--<br>
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