C Johnson wrote:
Sorry guys, I'm still learning the lingo.
I want to simulate multiple molecules.
This is what I tried:
genconf -f polygly.pdb -nbox 2 2 2 -shuffle -o did_it_work.pdb
Does this even seem like the right thing to do?
I don't see the need for -shuffle, but yes, that's more or less the right way to
create an 8-peptide grid.
I got to this part:
grompp -v -f em -c b4em -o em -p speptide
mdrun -v -s em -o em -c after_em -g emlog
But I get an error that essentially tells me that my system needs to be
energy minimized:
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 150 ]
I'm guessing I'm pretty wrong in my approach to adding multiple
molecules based on a single molecule pdb file. I'm determined to get
this :)
Well, what's in your em.mdp file? It could be that there is horrendous atomic
overlap that even EM can't resolve. But you can easily determine that by
looking at the coordinate file that you used as input into grompp. I don't see
the relationship to the system you build (did_it_work.pdb) and the coordinate
file passed to grompp (b4em), so it could be that something you did in between
messed up the system, but in that case you haven't told us everything you've
done and it makes it hard (impossible) to give you solid advice.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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