[gmx-users] Re Multiple Chains

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 16 02:39:39 CEST 2010

C Johnson wrote:
> Sorry, I sent the wrong steps.  This is what I did in order to get the 
> range checking error:
> genconf -f polygly.pdb -nbox 2 2 2 -shuffle  -o did_it_work.pdb
> pdb2gmx -f did_it_work.pdb -p did_it_work.top -o did_it_work
> 0: GROMOS96 43a1 force field

Were all of your termini treated correctly here?  If you pass multiple chains to 
pdb2gmx, the potential problem is that pdb2gmx will read the entire structure as 
one protein, thus trying to connect sequential N- and C-termini.  This is why 
the example on the wiki is pertinent - generate a topology for a single 
polypeptide, then (in your case) change the [molecules] section to reflect the 
fact that you're building a system with 8 protein molecules (instead of just 1). 
  Use the pdb2gmx-processed coordinate file as input into genconf and so forth.


> editconf -f did_it_work -o -d 1.0
> genbox -cp out -cs -p did_it_work -o b4em
> grompp -v -f em -c b4em -o em -p did_it_work
> The em.mdp is from the speptide tutorial.
> mdrun -v -s em -o em -c after_em -g emlog
> 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 ]
> Thanks guys for your help and sorry if I'm frustrating you.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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