[gmx-users] Range checking error
011013021-Jyotsna
011013021 at bioinfo.sastra.edu
Thu Feb 11 10:16:18 CET 2010
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
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
-------------------------------------------------------
Program mdrun_d, VERSION 4.0
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 .. 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
>> http://folding.bmc.uu.se>--
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