[gmx-users] Not enough memory. Failed to realloc
RAHUL SURESH
drrahulsuresh at gmail.com
Tue Nov 28 05:38:54 CET 2017
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
>>>>
>>>> ==================================================
>>>>
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>>>> Gromacs Users mailing list
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>>>>
>>>
>>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
>>
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>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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