[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
[gmx-users] make index
Hi everybody, I want to make an index with make_ndx. But when I just wanted to group SOL and CL and Protein and DPPC it tells me when I want to run grompp afterwards that there are some residues not indexed. I thought that that might be because the NA-ions are not grouped. But when I want to group them together with the SOL and the CL with the command 14|15|17 and run grompp afterwards it tells me that the index SOL_Cl could not be found. That is reasonable since my group is called: NA_CL_SOL So my question is: how can I rename such a index group? Bests, Eva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
On 6/27/12 11:08 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to make an index with make_ndx. But when I just wanted to group SOL and CL and Protein and DPPC it tells me when I want to run grompp afterwards that there are some residues not indexed. Copying and pasting an error message is much more effective. I could guess at what this error is, but seeing it would be more useful. I thought that that might be because the NA-ions are not grouped. But when I want to group them together with the SOL and the CL with the command 14|15|17 and run grompp afterwards it tells me that the index SOL_Cl could not be found. That is reasonable since my group is called: NA_CL_SOL So my question is: how can I rename such a index group? The names specified in the .mdp file and .ndx files must match, so you can either change the names in the .mdp file (easiest), use a text editor to modify the name of the group in the .ndx file (same principle, probably a little more scrolling and/or find and replace), or use make_ndx to rename the groups (not very efficient in this case). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] make index group
Dear all, I'm trying to perform order parameter analysis. I 've use :- make_ndx_d -f xxx.tpr -o sn1.ndx 15 a Cxx |... q i've got this error :- Group 15 not exist. I did not make index before I proceed with grompp for the mdrun, is it cause by this? thanks. Regards, bing ___ 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] make index group
Bing Bing wrote: Dear all, I'm trying to perform order parameter analysis. I 've use :- make_ndx_d -f xxx.tpr -o sn1.ndx 15 a Cxx |... q i've got this error :- Group 15 not exist. So use a group that does exist. If you're copying an index group creation recipe from some tutorial, go back to that and understand what this step is designed to achieve, and then adjust it to suit your new context. 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] make index group
Mark Abraham wrote: Bing Bing wrote: Dear all, I'm trying to perform order parameter analysis. I 've use :- make_ndx_d -f xxx.tpr -o sn1.ndx 15 a Cxx |... q i've got this error :- Group 15 not exist. So use a group that does exist. If you're copying an index group creation recipe from some tutorial, go back to that and understand what this step is designed to achieve, and then adjust it to suit your new context. In addition to Mark's advice, please see the wiki page for g_order; it explains exactly how to create the necessary index groups. If you're merging groups on into one, as it appears you are, you're doing it wrong. http://oldwiki.gromacs.org/index.php/g_order -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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
