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 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
