.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.
Thanks, Majid ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sat, April 9, 2011 7:18:30 PM Subject: Re: [gmx-users] Dangling bond error for dna majid hasan wrote: > Dear All, > > I created .pdb file for dna using gabedit. But when I try to create the >topology file I get this error: Fatal error: > 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. > > Output of pdb2gmx, and my input pdb files are attached. Could anyone please >suggest why this is happening? > Nothing is attached. -Justin > Thanks, > Majid > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
dna6_atomsremoved.pdb
Description: Binary data
dangling bond error_output of pdb2gmx
Description: Binary data
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