[gmx-users] Not enough memory. Failed to realloc
RAHUL SURESH
drrahulsuresh at gmail.com
Tue Nov 28 05:55:12 CET 2017
Dear Justin
It worked. Actually by its own. I reconstructed the pdb and gave again.
Thank you so much for your time
On Tue, Nov 28, 2017 at 10:08 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:
> This error occur only for this particular pdb structure. The protein here
> is attached with a metal ion. The necessary changes are made to the
> charmm36 ff.
>
> Should be some error in my pdb?
>
> On Tue, Nov 28, 2017 at 10:04 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
>> Here i have added the report for the commands
>>
>>
>> Command line:
>> *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
>>
>> Read 628 atoms
>> Volume: 579.929 nm^3, corresponds to roughly 260900 electrons
>> No velocities found
>> system size : 3.716 91.693 1.702 (nm)
>> diameter : 91.698 (nm)
>> center : -0.048 0.153 0.001 (nm)
>> box vectors : 3.715 91.693 1.702 (nm)
>> box angles : 90.00 90.00 90.00 (degrees)
>> box volume : 579.93 (nm^3)
>> shift : 46.897 46.696 46.848 (nm)
>> new center : 46.849 46.849 46.849 (nm)
>> new box vectors : 93.698 93.698 93.698 (nm)
>> new box angles : 90.00 90.00 90.00 (degrees)
>> new box volume :822615.31 (nm^3)
>>
>>
>> Command line:
>> *gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro*
>>
>> Reading solute configuration
>> GROup of MAchos and Cynical Suckers
>> Containing 628 atoms in 43 residues
>> Reading solvent configuration
>> 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
>> Containing 648 atoms in 216 residues
>>
>> Initialising inter-atomic distances...
>>
>> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>> based on residue and atom names, since they could not be
>> definitively assigned from the information in your input
>> files. These guessed numbers might deviate from the mass
>> and radius of the atom type. Please check the output
>> files if necessary.
>>
>> NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
>> from the source below. This means the results may be different
>> compared to previous GROMACS versions.
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> A. Bondi
>> van der Waals Volumes and Radii
>> J. Phys. Chem. 68 (1964) pp. 441-451
>> -------- -------- --- Thank You --- -------- --------
>>
>> Generating solvent configuration
>> Will generate new solvent configuration of 51x51x51 boxes
>> Solvent box contains 83316213 atoms in 27772071 residues
>>
>> -------------------------------------------------------
>> Program: gmx solvate, version 2016.4
>>
>> Memory allocation failed:
>> std::bad_alloc
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> On Mon, Nov 27, 2017 at 11:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 11/27/17 11:26 AM, RAHUL SURESH wrote:
>>>
>>>> Hi
>>>>
>>>>
>>>>
>>>> *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
>>>>
>>>
>>> And how large is the resulting box? Are all the coordinates properly
>>> defined? What is the full screen output of gmx solvate up to the failure?
>>>
>>> -Justin
>>>
>>>
>>> I have used the above command to generate the box. Infact I have used
>>>> this
>>>> command before and I never got any error.
>>>>
>>>> Thank you
>>>>
>>>> On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>> On 11/27/17 7:17 AM, RAHUL SURESH wrote:
>>>>>
>>>>> Dear Users
>>>>>>
>>>>>> I am trying to carryout protein-metal interaction using charmm36 ff.
>>>>>> During
>>>>>> solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
>>>>>> solv.gro"
>>>>>> *i receive a error stating
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes
>>>>>> for
>>>>>> atoms_->atom,atoms_->atom=0(called from
>>>>>> file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/
>>>>>> topology/atomsbuilder.cpp,line
>>>>>> 86)". *
>>>>>> I have enough space to carry out this simulation and I am using 2016
>>>>>> version of gromacs.
>>>>>>
>>>>>> How large is your box? Are you sure you have set its size in nm, not
>>>>> A?
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Assistant Professor
>>>>> Virginia Tech Department of Biochemistry
>>>>>
>>>>> 303 Engel Hall
>>>>> 340 West Campus Dr.
>>>>> Blacksburg, VA 24061
>>>>>
>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>
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>>>>> * For (un)subscribe requests visit
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>>
>>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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>>>
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>>>
>>
>>
>>
>> --
>> *Regards,*
>> *Rahul Suresh*
>> *Research Scholar*
>> *Bharathiar University*
>> *Coimbatore*
>>
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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