[gmx-users] Re: Protein ligand simulation

[Mark Abraham]

On 2/12/2011 3:41 PM, bharat gupta wrote:
> Yes, but I took the coordinates for phosphate ion from some other pdb 
> file and docked with my protein using autodock. Then I generated the 
> parameter for the ion using swissparam. Then prepared the protein file 
> using pdb2gmx and pasted the coordinates of docked ion from the docked 
> file obtained from autodock. What Shall I do now ?? ...

Don't paste apples with oranges and feed them to a program in a format 
that specifies only apples. Convert the units.

Mark

>
> On Fri, Dec 2, 2011 at 1:35 PM, Dallas Warren 
> <Dallas.Warren at monash.edu <mailto:Dallas.Warren at monash.edu>> wrote:
>
>     One file you used had the coordinates in angstroms, the other in
>     nanometers.
>
>     You cannot have numbers with different units in the same
>     coordinate file.  Which is what you did.  Hence why they are not
>     in the locations you assumed they were.
>
>     Catch ya,
>
>     Dr. Dallas Warren
>
>     Medicinal Chemistry and Drug Action
>
>     Monash Institute of Pharmaceutical Sciences, Monash University
>     381 Royal Parade, Parkville VIC 3010
>     dallas.warren at monash.edu <mailto:dallas.warren at monash.edu>
>
>     +61 3 9903 9304
>     ---------------------------------
>     When the only tool you own is a hammer, every problem begins to
>     resemble a nail.
>
>     *From:*gmx-users-bounces at gromacs.org
>     <mailto:gmx-users-bounces at gromacs.org>
>     [mailto:gmx-users-bounces at gromacs.org
>     <mailto:gmx-users-bounces at gromacs.org>] *On Behalf Of *bharat gupta
>     *Sent:* Friday, 2 December 2011 3:22 PM
>     *To:* jalemkul at vt.edu <mailto:jalemkul at vt.edu>; Discussion list
>     for GROMACS users
>     *Subject:* Re: [gmx-users] Re: Protein ligand simulation
>
>     I didn't understand what you meant by that link. Can you please
>     tell me what can be done ??
>
>     On Fri, Dec 2, 2011 at 11:52 AM, Justin A. Lemkul <jalemkul at vt.edu
>     <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     bharat gupta wrote:
>
>     Sorry I didn't understand . Can u brief it ??
>
>     I already did:
>
>     http://lists.gromacs.org/pipermail/gmx-users/2011-December/066664.html
>
>     -Justin
>
>     On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul <jalemkul at vt.edu
>     <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>     <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
>        bharat gupta wrote:
>
>            Yes, I prepared the protein file separately using pdb2gmx and
>            then I pasted the ligand manually from the docked file.
>
>
>        Then you prepared it incorrectly.  You need to use the right units.
>
>        -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> <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>
>
>        ==============================__==========
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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
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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 <http://vt.edu> | (540) 231-9080
>     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>
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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>
>
>
>

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