Re: [gmx-users] Conformation search!
Dear Anthony, You can apply distance restraints to pairs of atoms, e.g. CA atoms in your domains. Check the manual. Ran. Anthony Cruz wrote: On Thursday 17 April 2008 9:13 pm, Mark Abraham wrote: Anthony Cruz wrote: Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure feature present. I was thinking in use some position restrain in the backbone atoms of the domains and leave the linkers and all the side chains to move freely but this aproach will not let the system to change the conformation. I'm using GROMACS 3.2.1. With a dihedral constraint it will be posible to what I want to do? How can I do it? There is any other option to do this? This didn't get an answer earlier this week, probably because of the way you've worded it. It's a bad idea to presuppose things about the solution in your description, because if you're right then people wonder why you are being lazy and not trying it out, and if you're wrong then you're distracting people from identifying the real solution... see http://catb.org/~esr/faqs/smart-questions.html#symptoms You seem to want to let your domains move relative to each other, but also to deny them much internal freedom. So what you want to do is enforce (some of) their internal structure. Thus, use distance restraints. Mark Thank you for your answer. But probably I don't make my point clear. I have a protein with two units (domains). I think that distant restraint will restraint the distance between the two domains or units... This is done by the linkers between them. I want them to move freely but not to change its structure, like freezing the backbone and let the rest to move freely. How I could do this? I think that I explain my problem better this time. I presuppose things about the solution because I don't want that the people in the mailing list think that I just have the problem and not try to resolve it my self. Thank you for your advise Mark I will try to change the way I make the questions. Anthony ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Conformation search!
Anthony Cruz wrote: You seem to want to let your domains move relative to each other, but also to deny them much internal freedom. So what you want to do is enforce (some of) their internal structure. Thus, use distance restraints. Mark Thank you for your answer. But probably I don't make my point clear. I have a protein with two units (domains). I think that distant restraint will restraint the distance between the two domains or units... This is done by the linkers between them. I want them to move freely but not to change its structure, like freezing the backbone and let the rest to move freely. How I could do this? Distance restraints to enforce their *internal structure*... So don't restrain all the distances, just some cunningly chosen ones inside each domain. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Conformation search!
Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure feature present. I was thinking in use some position restrain in the backbone atoms of the domains and leave the linkers and all the side chains to move freely but this aproach will not let the system to change the conformation. I'm using GROMACS 3.2.1. With a dihedral constraint it will be posible to what I want to do? How can I do it? There is any other option to do this? Best Regards, Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Conformation search!
Anthony Cruz wrote: Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure feature present. I was thinking in use some position restrain in the backbone atoms of the domains and leave the linkers and all the side chains to move freely but this aproach will not let the system to change the conformation. I'm using GROMACS 3.2.1. With a dihedral constraint it will be posible to what I want to do? How can I do it? There is any other option to do this? This didn't get an answer earlier this week, probably because of the way you've worded it. It's a bad idea to presuppose things about the solution in your description, because if you're right then people wonder why you are being lazy and not trying it out, and if you're wrong then you're distracting people from identifying the real solution... see http://catb.org/~esr/faqs/smart-questions.html#symptoms You seem to want to let your domains move relative to each other, but also to deny them much internal freedom. So what you want to do is enforce (some of) their internal structure. Thus, use distance restraints. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Conformation Search with Gromacs
Dear USERS, Can one use Gromacs for conformation search? If yes, how? Thanks, Adama _ Adama Tandia Modeling Simulation Corning INC SP-TD-01-01 Corning, NY (USA) Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Conformation Search with Gromacs
Tandia, Adama wrote: Dear USERS, Can one use Gromacs for conformation search? If yes, how? If you mean systematic search the answer is no. You can do energy minimization or MD. Thanks, Adama _ Adama Tandia Modeling Simulation Corning INC SP-TD-01-01 Corning, NY (USA) Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] conformation search
On Sat, 29 Apr 2006 08:13:33 +0800 Rongliang Wu [EMAIL PROTECTED] wrote: Hello, gmx-users， is it possible to do conformation searches using gromacs? and how? What do you mean by conformation searches ? XAvier Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-04-29 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
