Dear Experts, Hi from a beginner in Gromacs, I am trying to simulate i-motif so I have primed all the four chains and manually created a phosphodiester bond between two i-motif units. all the with Amber/Gromos ff the problem is :
Fatal error: Atom P in residue DT 1 was not found in rtp entry DT5 with 30 atoms while sorting atoms. while Charmm36ff - 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. while it works well if I use non primed i-motif and only single unit. I am very new to gromacs and I have only done some simulations of Proteins. I am in serious trouble..help required at large scale :) Thank You All Raghav
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