[gmx-users] ERROR: box vectors is shorter than twice the cut-off

[Michele Fuortes]

Hi,

I have installed gromacs-3.2.0_beta1 on a Macintosh with OS 10.3, and
everything seemed to work well.
No I'm trying to get the surface potential for a protein that I have
modeled on a similar protein which has a crystal structure with
swiss-model. The original protein file runs well.
But if I try to run the modeled protein (with the default .mdp file
settings) I get:

ERROR: One of the box vectors is shorter than twice the cut-off length.
Increase the box size or decrease rcoulomb.

or if I decrease the rcoulomb

ERROR: One of the box vectors is shorter than twice the cut-off length.
Increase the box size or decrease rlist.

then if I decrease the rlist I get the first error again. I am a little
baffled because the two protein are quite similar and if I look at the pdb
file there are same size.
I think it could be a problem with a mis-formatted pdb file.
Does anyone have a suggestion on what to do, or where to look. Note that I
am quite a novice with gromacs, please be patient ;-). I searched the list
archives but could not find an answer.


Thanks

Michele
-- 





--
Michele Fuortes, M.D., Ph.D.
Assistant Professor
Departments of Surgery and of Cell and Developmental Biology
Cornell University  - Weill Medical College
E-mail: mfuortes at REMOVETHISmed.cornell.edu