[gmx-users] Re: Protein ligand simulation

[bharat gupta]

Actually I check the file newbox.gro in VMD and I found that the phosphate
ion instead of being docked to my protein lies somewhere far away from the
protein. The docked complex was taken from autodock's docking result. So
what could have wrong . I guess this could be the reason for the box being
too large .

On Fri, Dec 2, 2011 at 10:54 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> bharat gupta wrote:
>
>> Hi,
>>
>> I am trying the simulation of a docked complex of my protein . While
>> solvating the box using the following command :-
>> genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>>
>>
>> The processing does not stop and continues to run . Here's the output
>> that I got while solvating the box , which is still continuing :-
>>
>>
>> Reading solute configuration
>> GRoups of Organic Molecules in ACtion for Science
>> Containing 3620 atoms in 231 residues
>> Initialising van der waals distances...
>>
>> WARNING: masses and atomic (Van der Waals) radii will be determined
>>         based on residue and atom names. These numbers can deviate
>>         from the correct mass and radius of the atom type.
>>
>> Reading solvent configuration
>> "216H2O,WATJP01,SPC216,SPC-**MODEL,300K,BOX(M)=1.86206NM,**WFVG,MAR.
>> 1984"
>> solvent configuration contains 648 atoms in 216 residues
>>
>> Initialising van der waals distances...
>> Will generate new solvent configuration of 46x46x46 boxes
>> Generating configuration
>> Sorting configuration
>> Found 1 molecule type:
>>    SOL (   3 atoms): 21024576 residues
>> Calculating Overlap...
>> box_margin = 0.315
>> Removed 1047843 atoms that were outside the box
>>
>> What have gone wrong for solvation to take this much time on 12
>> processors CPU.
>>
>
> genbox is not parallelized; you can only use 1 CPU.
>
> You've added 21 million water molecules (yikes!) to the box and genbox is
> trying to remove over 1 million atoms - I'd say your box is much too large
> for a solute of 3620 atoms, by several orders of magnitude.  You're
> probably running out of memory to do this operation.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
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> ICTAS Doctoral Scholar
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> Department of Biochemistry
> Virginia Tech
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> jalemkul[at]vt.edu | (540) 231-9080
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
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South Korea
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