[gmx-users] Re: Protein ligand simulation

[bharat gupta]

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 ?? ...

On Fri, Dec 2, 2011 at 1:35 PM, Dallas Warren <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****
>
> +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] *On Behalf Of *bharat gupta
> *Sent:* Friday, 2 December 2011 3:22 PM
> *To:* 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> 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>> 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****
>
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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
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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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> --
> 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
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>
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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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