but using docking I have to fix the grid and have to dock at that position... which is not my objective ... I want the peptide to come and bind own its own to the protein... I have heard of full body dock , in which there is no need to define grid points , will that be useful ??
On Mon, Apr 11, 2011 at 2:02 PM, Thomas Evangelidis <teva...@gmail.com>wrote: > You can try Rosetta for flexible peptide docking. > > > > On 11 April 2011 15:32, Mark Abraham <mark.abra...@anu.edu.au> wrote: > >> Hi, >>> >>> I want to know how can I predict where a designed peptide will bind to my >>> protein target or not using simulation ... Can anybody guide me ?? >>> >> >> I don't think anybody has the computational resources to answer this >> question with unguided MD. Docking programs are probably the way to get a >> guide about what binding modes might be reasonable, but I don't know what >> software might be fit for the purpose. >> >> Mark >> -- >> gmx-users mailing list 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. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tev...@bioacademy.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > -- > gmx-users mailing list 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. > 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
-- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists