[gmx-users] Re: dangling bond at at one of the terminal ends

ramaraju801 ramaraju801 at gmail.com
Sun Jun 3 15:47:54 CEST 2012

HI, everyone

am working on a system consisting of protein-DNA complex,where an protein
comes and binds to the DNA to form a complex. To produce an topology file in
gromacs i gave the command "  pdb2gmx -f XXX.pdb -o XXX.gro -p XXX.top -ter 
-ignh -ff amber99 " .

its creating the topology files of the protein but when its starts creating
the topology file for the DNA seq its recognizing the starting and the
ending terminus residue. and then stops giving an 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." 

i tried editing the .n.tdb and .c.tbd files by writing the terminal residues
of DNA in those files but then its giving an error which says need an
directive before the residue must been and old file 

plz help,


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