Several questions come to mind, aside from trying to sift through your
interpretation of error messages. Hint: always show your exact command,
followed by the relevant portion of the screen output; that way we don't
have to guess what you've been up to :-)
1. Do you have two different proteins, or are they the same? If they
are different, changing the number of Protein molecules in your topology
will not be correct. If they are the same, this is fine.
2. Does the order of your topology follow the order of the coordinate
file? When you get warnings about non-matching atom names, you should
be alert that something has gone wrong.
-Justin
kartik mehra wrote:
Dear GMX Users,
I am trying to set up a simulation box with two proteins. I have
perused the archives about the methodology of doing so. I tried the
recommended option of changing the number of protein molecules in the
topology file to 2. However when I run grompp after editconf and
genbox, I get warning that the number of co -ordinates do not match
(since I had not updated the number of solvent molecules ...) After
updating the number of solvent molecules, when I try running grompp
again, it shows a warning that the 23644 atom names do not match in
top and gro files and that atom names from top files are being chosen .
Upon subsequent mdrun, the system explodes after a 1-4 interaction
warning.
I was wondering whether anyone could help me out on this ... I do
understand that the topic has been discussed pretty often but would
appreciate any help ...
Cheers
Kartik
PS: I have not yet tried the other suggestion of translation and
rotation followed by concatenating the two files
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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