[gmx-users] Re: Protein ligand simulation

Fri Dec 2 03:14:53 CET 2011

I checked the docked structure and the structure obtained after adding the
ligand coordinates to the processed file obtained after using pdb2gmx
command. It's very surprising that in the docked structure ligand is at the
correct place but the processed gromacs file the ligand lies far apart from
the protein. Any clue what could be the reason for this ??

On Fri, Dec 2, 2011 at 11:00 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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://vt.edu/Pages/Personal/justin>
>>    <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
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>>
>>
> --
> ==============================**==========
>
> 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<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
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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