On 17/09/2012 2:55 AM, vidhya sankar wrote:
Dear Mark ,
Again Thanks for you reply
After Editing my pdb file from intial FXXXXL to FXXXXLF format
Then i Run pdb2gmx for my linaer pdb file , i have selected none for both
termini ( with -ter option) as you mailed me in the previous mail
I have got error as follows
Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper
terminal entry.
How to Rectify this error
That suggests you have a problem with your coordinate file that is
independent of your attempt to cyclize. Can you generate a topology for
FXXXXL with a) -ter choosing none, b) -ter choosing anything else?
Mark
For your Remembrance i pasted your previous Discussion
1) Take your initial coordinate file, make a copy and in it make a copy
of the first residue and place it after the last residue, taking care to
obey the format of the file you're using, and update things like atom
counts and atom and residue indices. The coordinates of the copied atoms
don't matter. Now you have a coordinate file for FXXXXLF.
2) Process that with pdb2gmx using -ter and choosing "none". This has
built a linear topology for FXXXXLF, with a correct L-to-F link for you
to use as a template for making a cyclic FXXXXL.
Thanks in Advance
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