[gmx-users] x2top - is it just me?
etron at shefayim.org.il
Sat Jan 26 18:44:47 CET 2002
I am trying to run x2top on .gro files I created
from genbox by the command:
genbox -cp wedge.gro -ci wedge.gro -o 12wedge.gro -nmol 11 -box 30 30 1
I am doing this because I want to see the interactions between
12 molecules of this wedge.
now, this creates a fine .gro file, but if i want to run grompp
on it I also need a topolgoy file
there is a -p option to genbox for a .top file which is supposed
to be both input and output - I didnt understand how this could
be, but anyway it won't create me a new .top file - just complain
if it doesnt exist, so I guess this is not really an output option.
so the thing to do is probably x2top on the .gro file,
but I cant get it to work - it just gets stuck after reporting
the number of type to mass conversions and atom 40.
I didn't think it should take long, and 10 minutes seems more
I also tried PRODRG, which is actually what created the wedge.gro
file, but it didnt read the 12wedge.gro file
I am trying simple carbon molecules, which, I admit,
are not textbook examples of how carbon behaves,
but I shouldnt think this is the problem
can anyone help?
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