[gmx-users] DNA dangling bond

Nuria Alegret nuria.alegret at urv.cat
Tue Oct 4 20:10:32 CEST 2011

I'm using gromacs version 4.0.5. My system is a double stranded DNA (9 
nucleotides), a bit modified (the DC3 terminal is replaced by another 
one named C5l). When I try to convert the pdb file to a .gro one, a 
message error appear, as follows:
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.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors/

Can someone please help?? I was not able to find a solution.... Thanks 
in advance!!

I attach the pdb file.

Nuria Alegret
University Rovira i Virgili (Spain)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111004/77eaddce/attachment.html>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: dsDNA_fr578.pdb
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111004/77eaddce/attachment.ksh>

More information about the gromacs.org_gmx-users mailing list