[gmx-users] Re: Protein ligand simulation

[Dallas Warren]

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<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
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   Virginia Tech
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   jalemkul[at]vt.edu<http://vt.edu> <http://vt.edu> | (540) 231-9080
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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
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E-mail : monu46010 at yahoo.com<mailto:monu46010 at yahoo.com> <mailto: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<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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