[gmx-users] Acetyl capping and Range checking error

[Justin A. Lemkul]

Quoting Mauro Puppett <esagono at hotmail.com>:

>
> Hi all,
> I'm trying to run the simulation of a proline with an acetyl group on the N
> terminus and an NH2 on the C.
> I've already chenged the name of the residues on the pdb file, this way:
> HETATM    1 N    PRO     1      -0.650  -0.337   0.028
> HETATM    2 CA   PRO     1       0.700  -0.304  -0.532
> HETATM    3 HA   PRO     1       0.634  -0.117  -1.630
> HETATM    4 CB   PRO     1       1.186  -1.746  -0.265
> HETATM    5 HB1  PRO     1       1.743  -1.795   0.701
> HETATM    6 HB2  PRO     1       1.848  -2.144  -1.071
> HETATM    7 CG   PRO     1      -0.109  -2.560  -0.104
> HETATM    8 HG1  PRO     1       0.043  -3.520   0.445
> HETATM    9 HG2  PRO     1      -0.525  -2.790  -1.115
> HETATM   10 CD   PRO     1      -1.046  -1.592   0.637
> HETATM   11 HD1  PRO     1      -2.109  -1.878   0.465
> HETATM   12 HD2  PRO     1      -0.827  -1.548   1.730
> HETATM   13 C    PRO     1       1.650   0.724   0.080
> HETATM   14 O    PRO     1       2.846   0.576   0.058
> HETATM   15 N    NH2     1       1.140   1.851   0.659
> HETATM   16 H1   NH2     1       0.142   2.048   0.638
> HETATM   17 H2   NH2     1       1.837   2.497   1.025
> HETATM   18 CH3  ACE     1      -2.970   0.591   0.323
> HETATM   19 HH31 ACE     1      -2.983   0.374   1.415
> HETATM   20 HH32 ACE     1      -3.524   1.545   0.167
> HETATM   21 HH33 ACE     1      -3.526  -0.201  -0.227
> HETATM   22 C    ACE     1      -1.543   0.704  -0.194
> HETATM   23 O    ACE     1      -1.220   1.712  -0.778
>
> Every's fine till I try to use the command mdrun, after preprocessing with
> gromp with the pr.mdp.
> I get this error:
>
> 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.

So is this a position-restrained MD step, or some sort of position-restrained
minimization?  Hint: providing your .mdp file will help us out a lot in
diagnosing your problem :-)

If you already did energy-minimization, did you get a reasonable potential
energy?  The mdrun message is giving you some clues ("collisions", "parameter
errors") which could be interpreted as poor initial starting structure, broken
topology, etc.  Load the trajectory into a program like VMD and see where
things start to fall apart.

Also, read here:

http://wiki.gromacs.org/index.php/blowing_up

...as well as searching the list archive to see what others have done.  This is
a common error that people report.

-Justin

>
> Variable ci has value -2147483648. It should have been within [ 0 .. 125 ]
>
> How could I solve the problem?
> Should I modify something else other than the pdb?
> Thanks in advance
>
> Mauro Puppett
>
>
>
>
>
>
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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/

========================================