[gmx-users] Range checking error

[Justin A. Lemkul]

011013021-Jyotsna wrote:
> 
> Dear all,
> 
> I am simulating a protein along with a ligand molecule. The ligand 
> molecule is modeled as per the literature. The ligand molecule consists 
> of FE and S alone and in addition to that it is covalently bonded with 
> the enzyme's cys residue. So I have modeled my ligand FE4S4 with SG and 
> CB atoms of cystine. I have included only bonded terms in my forcefield 
> for my ligand (since I do not know other terms like angle and dihedral 
> angles force constants etc) and the article does not mention these.
> 
> Now the problem is, when I try to run energy minimization , I encounter  
> "Range checking error:" and the detailed error is pasted below. So I 
> suspect this error is due to inadequate force field data like angles and 
> dihedrals. Or is it caused by some other factor?.But one thing I am sure 

More likely the underlying physics is unreasonable.  See here:

http://www.gromacs.org/Documentation/Errors#Range_Checking_error

> of is , when I simulate my system without the ligand, the error 
> disappears. I am unable to find any answer to this query in the forum.
> 
> Kindly extend your help this time as you always do.
> 
> 
> #########################################################################
> Steepest Descents:
>    Tolerance (Fmax)   =  2.00000e+02
>    Number of steps    =         5000
> Warning: 1-4 interaction between 2446 and 2468 at distance 6.079 which 
> is larger than the 1-4 table size 2.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Step=    0, Dmax= 1.0e-02 nm, Epot=          nan Fmax= 1.71540e+115, 
> atom= 2452

You should have seen these errors in the list archive if you did a search.  Your 
system is clearly blowing up (see link above).  Your Fmax is essentially 
infinite, which is usually due to extreme atomic overlap, which should be clear 
in the input structure.  Otherwise, mdrun is giving you clues about atoms 2446 
and 2468 - start investigating there.

> -------------------------------------------------------
> Program mdrun_d, VERSION 4.0
> Source code file: nsgrid.c, line: 357
> 

I would also encourage you to upgrade to the latest version (4.0.7); it will not 
fix your problem, but there have certainly been some important bug fixes related 
to stability and usability that will make your life easier :)

-Justin

> 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 .. 4096 ]
> 
> ############################################################################# 
> 
> 
> Thank You
> Jyotsna
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Wed, 03 Feb 2010 22:42:09 +1100
>  Mark Abraham <mark.abraham at anu.edu.au> wrote:
>> *This message was transferred with a trial version of CommuniGate(r) Pro*
>>
>>
>> ----- Original Message -----
>> From: 011013021-Jyotsna <011013021 at bioinfo.sastra.edu>
>> Date: Wednesday, February 3, 2010 21:48
>> Subject: Re: [gmx-users] H2 topology
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>
>>>
>>> Dear David,
>>>
>>> Thanks for your reply.  From your reply, I get the impression that 
>>> the bond length of my hydrogen molecule gets adjusted duing 
>>> minimization of the whole system ( protien+water+ inserted hydrogen 
>>> molecule). But the issue impending is the insertion of the hydrogen 
>>> molecule itself into the protein+water box created in previous step. 
>>> For insertion/addition of hydrogen molecules I used the command:
>>>
>>> genbox_d -cp 2frv.conf.gro -o 2frv.solv.gro -p 2frv.top –ci h2.gro 
>>> –nmol 100
>>
>> What about a two-stage process? Do genbox -ci h2.gro -nmol 100 when 
>> there's no water, and then solvate *afterwards*.
>>
>> Or, generate solvent, and get a list of 100 random numbers in the 
>> right range, manually delete those water molecules to create 
>> interstices, update your [molecules] section, then use genconf -ci and 
>> equilibrate carefully to fix the density.
>>
>> Or, generate solvent for a box somewhat smaller than the one you want, 
>> use editconf -scale to scale the coordinates up to create interstices, 
>> use genconf -ci and then minimize really gently to fix all the bond 
>> lengths, and equilibrate carefully to fix the density.
>>
>> Mark
>>
>>>  It reports to me the inability to add any of the hydrogen molecules, 
>>> ie it adds 0 molecules out of 100 requested.
>>> ###########error########################
>>> Reading molecule configuration
>>> Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
>>> Containing 3 atoms in 1 residue
>>> Initialising van der waals distances...
>>> Try 999
>>> Added 0 molecules (out of 100 requested) of H2
>>> Writing generated configuration to 2frv.solv.gro
>>>
>>> Back Off! I just backed up 2frv.solv.gro to ./#2frv.solv.gro.1#
>>> PERIPLASMIC HYDROGENASE; PERIPLASMIC HYDROGENASE
>>>
>>> Output configuration contains 8340 atoms in 977 residues
>>> Volume : 1299.08 (nm^3)
>>> Density : 143.043 (g/l)
>>> Number of SOL molecules: 186
>>>
>>> Processing topology
>>> Removing line #40 'SOL 39308' from topology file (2frv.top)
>>> ####################error end###############
>>> How do i rectify this problem?
>>>  I suspect the problem is due to the bond length of the hydrogen 
>>> molecule that I created with 1.66A distance ( as described in my 
>>> previous post) and the fact that the gap between the solvent 
>>> molecules (in my case , water) is not big enough to accomodate the H2 
>>> molecules(as I had used the pdb of CO2 and replaced each O with an H 
>>> and C atom with dummy atom.). So could you please help me figure out 
>>> any tool that helps in adjusting the bond length of my hydrogen 
>>> molecule in pdb to the desired length of 0.7A.
>>>
>>> Or as you said is it possible to minize a single molecule using 
>>> md_run program, as I encountered certain problems in doing so .
>>>
>>> Sorry for the lengthy mail.
>>>
>>> Thank you ,
>>> Jyotsna
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Wed, 03 Feb 2010 09:30:21 +0100
>>>  David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>>> >*This message was transferred with a trial version of CommuniGate(r) 
>>> Pro*
>>> >On 2/3/10 7:52 AM, 011013021-Jyotsna wrote:
>>> >>
>>> >>Dear Justin ,
>>> >>
>>> >>Thank you very much for your help.
>>> >>To create a linear H2 molecule with a dummy atom in the center is
>>> >>proving to be quite a difficult task.
>>> >>Hence , I created a pdb file of CO2 using Cerius(2) , and replaced the
>>> >>atoms in the pdb file with 2 H atoms and a dummy atom.(since CO2 is a
>>> >>three atom , linear system i.e the two O atoms replaced by two H atoms
>>> >>and the C atom by the dummy)
>>> >>The problem is the bond distance. For CO2 , it is 1.66 A but I need 
>>> the
>>> >>distance for H2 to be only 0.7 A as per the literature I am 
>>> following.>>By replacing the atoms in the pdb file , there is a 
>>> problem regarding
>>> >>distance since the coordinates of the pdb also point towards 1.6 A.
>>> >>I would be very grateful if you could tell me how I can build a PDB 
>>> for
>>> >>H2 with dummy atom with the right distance.
>>> >>
>>> >>Thank You,
>>> >>Jyotsna
>>> >Doesn't matter if the pdb is wrong initially, you just do an energy 
>>> minimization. What is important is (put in exact bond length):
>>> >
>>> >[ bonds ]
>>> >1 2 1 0.74 500000
>>> >
>>> >[ vsites2 ]
>>> >3 1 2 1 0.5
>>> >
>>> >
>>> >
>>> >-- >David van der Spoel, Ph.D., Professor of Biology
>>> >Dept. of Cell & Molec. Biol., Uppsala University.
>>> >Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205. Fax: 
>>> +4618511755.>spoel at xray.bmc.uu.se    spoel at gromacs.org  
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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