[gmx-users] Simulation of Primed DNA

[raghav singh]

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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