[gmx-users] Minimization error
Hi Users, I performed a simple minimization for a protein complex in vacuum. Didn't get any error while performing the minimization but when visualised the pdb file after the minimization the chains of the protein complex separated. What could be the reason. Thanks, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- gmx-users mailing listgmx-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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Minimization error
1 check with the rtp files in your forcefield, especially the parameters 2 check with the imput pdb file, the format matters a lot. On Wed, Oct 19, 2011 at 8:18 AM, aiswarya.pa...@gmail.com wrote: Hi Users, I performed a simple minimization for a protein complex in vacuum. Didn't get any error while performing the minimization but when visualised the pdb file after the minimization the chains of the protein complex separated. What could be the reason. Thanks, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- gmx-users mailing listgmx-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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Minimization error
aiswarya.pa...@gmail.com wrote: Hi Users, I performed a simple minimization for a protein complex in vacuum. Didn't get any error while performing the minimization but when visualised the pdb file after the minimization the chains of the protein complex separated. What could be the reason. Please see FAQ #3 under the heading: http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization -Justin Thanks, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- 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 -- gmx-users mailing listgmx-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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Minimization error
Hi, All the parameters are ok, still i get the complex separated. On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya.pa...@gmail.com wrote: Hi Users, I performed a simple minimization for a protein complex in vacuum. Didn't get any error while performing the minimization but when visualised the pdb file after the minimization the chains of the protein complex separated. What could be the reason. Please see FAQ #3 under the heading: http://www.gromacs.org/**Documentation/FAQs#Analysis_**and_Visualizationhttp://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization -Justin Thanks, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Minimization error
On 20/10/2011 4:14 PM, aiswarya pawar wrote: Hi, All the parameters are ok, still i get the complex separated. Simulation parameters have nothing to do with the phenomena in the FAQ Justin pointed out to you. Please read it. Mark On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote: Hi Users, I performed a simple minimization for a protein complex in vacuum. Didn't get any error while performing the minimization but when visualised the pdb file after the minimization the chains of the protein complex separated. What could be the reason. Please see FAQ #3 under the heading: http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization -Justin Thanks, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- 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 listgmx-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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
