[gmx-users] Simulation of Primed DNA

[Justin A. Lemkul]

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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