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 <jalem...@vt.edu
<mailto:jalem...@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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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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
Pusan National University
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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
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