<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">.pdb file size was big, so message didn't deliver. Now I have removed atoms from pdb file to reduce the size, and the files are attached. <br><br>Thanks,<br>Majid<br><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sat, April 9, 2011 7:18:30 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Dangling bond error for dna<br></font><br>
<br><br>majid hasan wrote:<br>> Dear All,<br>> <br>> I created .pdb file for dna using gabedit. But when I try to create the topology file I get this error: Fatal error:<br>> There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file.<br>> <br>> Output of pdb2gmx, and my input pdb files are attached. Could anyone please suggest why this is happening?<br>> <br><br>Nothing is attached.<br><br>-Justin<br><br>> Thanks,<br>> Majid<br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><span><a target="_blank"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><span><a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>Please search the archive at <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br><span>Can't post? Read <a target="_blank"
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