[gmx-users] About topology construction for yclic pepetide
scvsankar_agr at yahoo.com
Sun Sep 16 18:55:50 CEST 2012
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
There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.
How to Rectify this error
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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