[gmx-users] problem with xtc in vmd
smilidon at mail2Cool.com
Fri Mar 24 09:14:34 CET 2006
i am just an intermediate guy with gromacs now.
i tried to view the final xtc file in vmd.
in the first protein, i was sucessful in viewing it.
In my second protein, it says error in number of atoms.so i had to
convert it in to a format with a xtc file having only the protein
molecules,according to a "dynatraj" website.
I did it with trjconv.It showed me a very bad output of only lines.
So i redid the whole process and got another output.The same problem
persists in vmd.
The important thing being that the outputs were viewable in ngmx under
i don't know where the problem is, is it in vmd or some bug in
trjconv.From the lines output, i think it has something to do with the
data for bond formation not being present in it.Is my prediction
i have done so much of experimentation that i now don't know what will
be ideal mdp file parameters for cytosolic proteins.Can someone send me
Thanks in advance.
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