[gmx-users] Protein going out of the box
Hello, When I am running energy minimisation of protein-peptide complex, minimised structure shows a space for the protein in water box; but peptide remains inside the box while protein is seen outside. Same occurs when I keep pbc = xyz and/or nstcomm = 1 in .top file, I am including individual posre.itp files (posre_A.itp and posre_B.itp) separately. How should I fix this problem ? Regards, Nikhil Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8.. http://downloads.yahoo.com/in/internetexplorer/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Protein going out of the box
nikhil damle wrote: Hello, When I am running energy minimisation of protein-peptide complex, minimised structure shows a space for the protein in water box; but peptide remains inside the box while protein is seen outside. Same occurs when I keep pbc = xyz and/or nstcomm = 1 in ..top file, I am including individual posre.itp files (posre_A.itp and posre_B.itp) separately. How should I fix this problem ? See this page, in particular the bottom. http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Protein going out of the box
Think outside of the box when using Periodic Boundary Conditions. :p Tsjerk On Wed, Jul 15, 2009 at 9:14 AM, Mark Abrahammark.abra...@anu.edu.au wrote: nikhil damle wrote: Hello, When I am running energy minimisation of protein-peptide complex, minimised structure shows a space for the protein in water box; but peptide remains inside the box while protein is seen outside. Same occurs when I keep pbc = xyz and/or nstcomm = 1 in ..top file, I am including individual posre.itp files (posre_A.itp and posre_B.itp) separately. How should I fix this problem ? See this page, in particular the bottom. http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions Mark ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Protein going out of the box
Try using trjconv. Look at the -pbc options and also maybe -center options. --Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Wed, Jul 15, 2009 at 10:09, nikhil damle pdnik...@yahoo.co.in wrote: but peptide remains inside the box while protein is seen outside. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
