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.war...@monash.edu <mailto:dallas.war...@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.war...@monash.edu <mailto:dallas.war...@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-boun...@gromacs.org <mailto:gmx-users-boun...@gromacs.org> [mailto:gmx-users-boun...@gromacs.org <mailto:gmx-users-boun...@gromacs.org>] *On Behalf Of *bharat gupta *Sent:* Friday, 2 December 2011 3:22 PM *To:* jalem...@vt.edu <mailto:jalem...@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 <jalem...@vt.edu <mailto:jalem...@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 <jalem...@vt.edu <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem...@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> ==============================__========== -- gmx-users mailing list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> http://lists.gromacs.org/__mailman/listinfo/gmx-users <http://lists.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org> <mailto:gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>>. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists>-- BharatPh.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 : monu46...@yahoo.com <mailto:monu46...@yahoo.com> <mailto:monu46...@yahoo.com <mailto:monu46...@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 ========================================-- gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- BharatPh.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 : monu46...@yahoo.com <mailto:monu46...@yahoo.com> -- gmx-users mailing list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
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