[gmx-users] Re: Protein ligand simulation

[Justin A. Lemkul]

bharat gupta wrote:
> 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 .
> 

Sounds like you chose Autodock's undocked complex where the protein and ligand 
are far apart, but that's more of an Autodock question rather than a Gromacs one.

-Justin

> On Fri, Dec 2, 2011 at 10:54 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
> 
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> 
> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
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> South Korea
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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

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