[gmx-users] Re: stepsize too small ... but potential energy negative!

[Anna Marabotti]

Dear Justin,
to add other elements to find a solution to this problem, I repeated all the
Gromacs procedure until minimization on the file PDB I used as template to
model my protein. pdb2gmx warns that 232 atoms have non-zero occupancy, it's
because there are sidechains with alternative conformations, but for the
rest everything is OK. When I try to launch the mdrun to minimize the
protein, however, the range checking error appears:
 
Reading file 1WBE_min.tpr, VERSION 4.0.7 (double precision)

Steepest Descents:

   Tolerance (Fmax)   =  1.00000e+03

   Number of steps    =        50000

 

-------------------------------------------------------

Program mdrun_d, VERSION 4.0.7

Source code file: nsgrid.c, line: 357

 

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 .. 1728 ]

 

So I think definitely that the problem is in the protein structure arising
from some bad coordinates in the template I used to model my protein.

I have to wait for the approval of people working on this project to send
you coordinates and topologies of my model, but since I think that the error
in the model is strictly derived from the error in this public file, I will
send you privately the coordinates and topologies of this file. Please
remember that in my model there are some atoms with occupancy <1, but the
conformation of the sidechains is unique. I corrected by hand the occupancy
on my model, re-tried to minimize it and nothing changed: the same error
occurs. On the contrary, in this case, with this template file, the mdrun
did not start at all.

 

Once again thank you very much and best regards

Anna

 
____________________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabotti at isa.cnr.it
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
 
"If you think you are too small to make a difference, try sleeping with a
mosquito"
 
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