[gmx-users] make index groups with make_ndx
Hi everybody, I want to make two index groups for my protein. The first one should contain the whole protein except of the residues : TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80 I tried it with the arguments: protein ! res 65 ! res 6 ! res 7 ! res 61 ! res 64 ! res 80 protein ! res 65 6 7 61 64 80 Both didn't work. The other index group should only contain the residues: TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80 Here I tried: res 6 res 7 res 61 res 64 res 65 res 66 This worked. So I don't understand why the negation of this command did not work in the first index group. Can you please help me? Thank you, Eva -- 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] make index groups with make_ndx
The selections are boolean (like a search). So to include both 6 and 7 you would use 6 | 7 (make the selection of 6 or 7) so you probably want something like ! res65 | ! res 6 etc. On 2012-09-18 10:56:14AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to make two index groups for my protein. The first one should contain the whole protein except of the residues : TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80 I tried it with the arguments: protein ! res 65 ! res 6 ! res 7 ! res 61 ! res 64 ! res 80 protein ! res 65 6 7 61 64 80 Both didn't work. The other index group should only contain the residues: TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80 Here I tried: res 6 res 7 res 61 res 64 res 65 res 66 This worked. So I don't understand why the negation of this command did not work in the first index group. Can you please help me? Thank you, Eva -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] make index groups with make_ndx
Thank you very much for your answer. I managed it now to get the right index groups. The selections are boolean (like a search). So to include both 6 and 7 you would use 6 | 7 (make the selection of 6 or 7) so you probably want something like ! res65 | ! res 6 etc. On 2012-09-18 10:56:14AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to make two index groups for my protein. The first one should contain the whole protein except of the residues : TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80 I tried it with the arguments: protein ! res 65 ! res 6 ! res 7 ! res 61 ! res 64 ! res 80 protein ! res 65 6 7 61 64 80 Both didn't work. The other index group should only contain the residues: TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80 Here I tried: res 6 res 7 res 61 res 64 res 65 res 66 This worked. So I don't understand why the negation of this command did not work in the first index group. Can you please help me? Thank you, Eva -- 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 -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst| KAUL 752A Genetics, Div. of Research| 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- 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
