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 [email protected] 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
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