raghav singh wrote:
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 :)
Nearly all common error messages (including these) are explained on the Gromacs
website:
http://www.gromacs.org/Documentation/Errors
In general, if there is no answer there, please search the list archives. Both
of these errors come up very frequently, as will most that you will likely
encounter.
Note that in your case, pdb2gmx is going to have a hard time generating a
topology, since in the i-motif there are numerous non-linear bonds. pdb2gmx is
only particularly well-suited for linear molecules, with very limited support
for branching. You will have to add entries in specbond.dat to create these
branched bonds. See the manual for implementation details, as well as:
http://www.gromacs.org/Documentation/File_Formats/specbond.dat
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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