[gmx-users] Acetyl capping and Range checking error

[Mauro Puppett]

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.

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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