> Then I tried to calculate RDF of Na+ solvating DNA using input
> ==>
> trajin md.traj 1 100 1
> radial rdf_DNA-Na+ 0.05 8.0 :Na+ :1-16
> go
> <==
...
> Set 100 Segmentation fault
>From the information in the e-mail to the list I cannot track the problem
and I am not able to reproduce it with (recent) versions of ptraj, or in
other words, I just calculated the RDF around a peice of DNA using both
ions and water and it seemed to work fine (in a single script) for me...
trajin md.traj 1 100 1
radial rdf_DNA-wat 0.05 8.0 :WAT :1-16
radial rdf_DNA-Na+ 0.05 8.0 :Na+ :1-16
Are you using a recent version of ptraj?
You can try dbx/gdb on the core file to see where the problem occurred(?)
Otherwise there is no obvious reason why the command should have failed.
Let me know if you have additional questions,
p.s. In my opinion, the RDF around a DNA may not be particularly useful
since DNA is not a radial molecule and has various different chemical
environments. You may get better information by looking at the RDF around
particular (individual) phosphate groups or hbond donors/acceptors in the
grooves, for example. Also, when looking at ion association, the RDF
around the whole DNA will not show you exactly where the ion is
interacting, only that it gets close to the DNA. Moreover, I imagine that
that RDF plot (of the ions) will be rather noisy due to poor statistics.
FYI, others have looked at proximal distributions functions (Beveridge and
co-workers) around particular groups. To get a better idea of water/ion
association, people have tended to visualize areas of high occupancy or
looked for specific ion/water interaction. The former is possible with
the "grid" command and the latter with the "hbond" functionality in ptraj
that keeps track of interactions between various atoms.
\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
| Departments of Medicinal Chemistry and of University of Utah
| Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
| & Center for High Performance Computing Salt Lake City, Utah 84112
|
| e-mail: tec3_at_utah.edu phone: (801) 587-9652 FAX: (801) 585-9119
\
http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418
Received on Wed Jul 17 2002 - 14:47:24 PDT
