On 31/05/2012 4:13 PM, ramaraju801 wrote:
when i ran gromacs to produce topology file for a nucleotide sequence it is
showing the above error saying "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".
... or maybe you need to use pdb2gmx correctly. Since you haven't told
us how you've used it, we can't help. Make sure you've done any
DNA-protein tutorials you can find, and applied any lessons you may learn.
i tried giving the starting and
ending residues in .n.tdb and .c.tdb files but it did not work with an
error saying "Fatal error:
reading termini database: directive expected before line:
P"
So you've broken the file format. Re-read the relevant part of chapter 5
of the manual and try again.
Mark
am uploading my PDB file of my DNA-protein compex sequence in which the
nucleotide sequence ranges from 15555 to 12216
http://gromacs.5086.n6.nabble.com/file/n4997922/dnaseq_rot1.pdb
dnaseq_rot1.pdb
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