[gmx-users] problem with xtc in vmd

smilidon theking smilidon at mail2Cool.com
Fri Mar 24 09:14:34 CET 2006

hi all,
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
all conditions.
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
Another query,
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.

<span id=m2wTl><p><font face="Arial, Helvetica, sans-serif" size="2" style="font-size:13.5px">_______________________________________________________________<BR>Get the FREE email that has everyone talking at <a href=http://www.mail2world.com target=new>http://www.mail2world.com</a><br>  <font color=#999999>Unlimited Email Storage &#150; POP3 &#150; Calendar &#150; SMS &#150; Translator &#150; Much More!</font></font></span>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060324/9d63a1fa/attachment.html>

More information about the gromacs.org_gmx-users mailing list