Quoting Mauro Puppett <[EMAIL PROTECTED]>:
>
> 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
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
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