Re: [gmx-users] make_ndx error
On 1/26/13 12:25 PM, Albert wrote: Hello: I am using make_ndx to make a index file in Gromacs 4.6, make_ndx -f input.pdb but it said: Copied index group 1 'Protein' Copied index group 25 'Water_and_ions' One of your groups is not ascending Group is empty What exactly did you enter at the make_ndx prompt? -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 * 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_ndx error
On 01/26/2013 06:53 PM, Justin Lemkul wrote: What exactly did you enter at the make_ndx prompt? -Justin 1|25 protein, water and ions -- 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_ndx error
On 1/26/13 1:30 PM, Albert wrote: On 01/26/2013 06:53 PM, Justin Lemkul wrote: What exactly did you enter at the make_ndx prompt? -Justin 1|25 protein, water and ions What types of ions do you have? I can reproduce this problem for a protein with ions bound to it, which are numbered discontinuously with water and ions in solution. -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 * 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_ndx error
On 01/26/2013 07:41 PM, Justin Lemkul wrote: What types of ions do you have? I can reproduce this problem for a protein with ions bound to it, which are numbered discontinuously with water and ions in solution. -Justin thank you for kind reply. I only have Na+ and Cl-. best Albert -- 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_ndx error
On 1/26/13 1:49 PM, Albert wrote: On 01/26/2013 07:41 PM, Justin Lemkul wrote: What types of ions do you have? I can reproduce this problem for a protein with ions bound to it, which are numbered discontinuously with water and ions in solution. -Justin thank you for kind reply. I only have Na+ and Cl-. Can you please post the following: 1. The groups printed in the make_ndx prompt 2. The output of gmxcheck on an index file created from your coordinate file (created simply by typing 'q' at the prompt, i.e. not creating any special groups) -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 * 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_ndx error
On 01/26/2013 07:51 PM, Justin Lemkul wrote: Can you please post the following: 1. The groups printed in the make_ndx prompt 2. The output of gmxcheck on an index file created from your coordinate file (created simply by typing 'q' at the prompt, i.e. not creating any special groups) -Justin make_ndx -f sys.pdb 0 System : 59870 atoms 1 Protein : 4746 atoms 2 Protein-H : 2329 atoms 3 C-alpha : 292 atoms 4 Backbone: 877 atoms 5 MainChain : 1170 atoms 6 MainChain+Cb: 1453 atoms 7 MainChain+H : 1455 atoms 8 SideChain : 3291 atoms 9 SideChain-H : 1159 atoms 10 Prot-Masses : 4746 atoms 11 non-Protein : 55124 atoms 12 Other : 18766 atoms 13 NMA : 6 atoms 14 POPC: 18760 atoms 15 CL :39 atoms 16 NA :34 atoms 17 Ion :73 atoms 18 NMA : 6 atoms 19 POPC: 18760 atoms 20 CL :39 atoms 21 NA :34 atoms 22 Water : 36285 atoms 23 SOL : 36285 atoms 24 non-Water : 23585 atoms 25 Water_and_ions : 36358 atoms gmxcheck_mpi -f md.xtc -n index.ndx Item#frames Timestep (ps) Step 1260.1 Time 1260.1 Lambda 0 Coords 1260.1 Velocities 0 Forces 0 Box1260.1 Contents of index file index.ndx -- Nr. Group #Entries FirstLast 0 System 59870 1 59870 1 Protein 4746 14752 2 Protein-H 2329 12332 3 C-alpha 292 82323 4 Backbone 877 22324 5 MainChain 1170 22325 6 MainChain+Cb1453 22326 7 MainChain+H 1455 24751 8 SideChain 3291 14752 9 SideChain-H 1159 12332 10 Prot-Masses 4746 14752 11 non-Protein551244745 59870 12 Other 187664745 23512 13 NMA647454750 14 POPC 187604753 23512 15 CL39 23513 23585 16 NA34 23518 23551 17 Ion 73 23513 23585 18 NMA647454750 19 POPC 187604753 23512 20 CL39 23513 23585 21 NA34 23518 23551 22 Water 36285 23586 59870 23 SOL36285 23586 59870 24 non-Water 23585 1 23585 25 Water_and_ions 36358 23586 23585 -- 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_ndx error
On 1/26/13 1:57 PM, Albert wrote: On 01/26/2013 07:51 PM, Justin Lemkul wrote: Can you please post the following: 1. The groups printed in the make_ndx prompt 2. The output of gmxcheck on an index file created from your coordinate file (created simply by typing 'q' at the prompt, i.e. not creating any special groups) -Justin make_ndx -f sys.pdb 0 System : 59870 atoms 1 Protein : 4746 atoms 2 Protein-H : 2329 atoms 3 C-alpha : 292 atoms 4 Backbone: 877 atoms 5 MainChain : 1170 atoms 6 MainChain+Cb: 1453 atoms 7 MainChain+H : 1455 atoms 8 SideChain : 3291 atoms 9 SideChain-H : 1159 atoms 10 Prot-Masses : 4746 atoms 11 non-Protein : 55124 atoms 12 Other : 18766 atoms 13 NMA : 6 atoms 14 POPC: 18760 atoms 15 CL :39 atoms 16 NA :34 atoms 17 Ion :73 atoms 18 NMA : 6 atoms 19 POPC: 18760 atoms 20 CL :39 atoms 21 NA :34 atoms 22 Water : 36285 atoms 23 SOL : 36285 atoms 24 non-Water : 23585 atoms 25 Water_and_ions : 36358 atoms gmxcheck_mpi -f md.xtc -n index.ndx Note that -f is not necessary to produce the needed information, just -n. Item#frames Timestep (ps) Step 1260.1 Time 1260.1 Lambda 0 Coords 1260.1 Velocities 0 Forces 0 Box1260.1 Contents of index file index.ndx -- Nr. Group #Entries FirstLast 0 System 59870 1 59870 1 Protein 4746 14752 2 Protein-H 2329 12332 Something is screwy here - note that gmxcheck finds that the index file has all of the protein heavy atoms first, then all of its hydrogens. Is that correct? It's certainly not normal for any structure processed by pdb2gmx. Besides the point, I suppose. 3 C-alpha 292 82323 4 Backbone 877 22324 5 MainChain 1170 22325 6 MainChain+Cb1453 22326 7 MainChain+H 1455 24751 8 SideChain 3291 14752 9 SideChain-H 1159 12332 10 Prot-Masses 4746 14752 11 non-Protein551244745 59870 12 Other 187664745 23512 13 NMA647454750 14 POPC 187604753 23512 15 CL39 23513 23585 16 NA34 23518 23551 17 Ion 73 23513 23585 18 NMA647454750 19 POPC 187604753 23512 20 CL39 23513 23585 21 NA34 23518 23551 22 Water 36285 23586 59870 23 SOL36285 23586 59870 24 non-Water 23585 1 23585 25 Water_and_ions 36358 23586 23585 Here's the issue. You've got a Water_and_ions group that has over 36k atoms, but it starts by counting backwards! 23586 to 23585 is a size of -1. When you inspect the index file in a text editor, what's in this group? -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 * 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_ndx
On 9/29/12 3:02 PM, Ali Alizadeh wrote: Dear All users make_ndx How to i can create a my especial index file? Is there a tutorial related to it? http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx Also, typing help at the prompt when running make_ndx provides examples and syntax information. -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 * 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_ndx: duplicates groups appearing in index.ndx file
On 7/31/12 10:14 AM, Laura Kingsley wrote: Hello, I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm having an issue with make_ndx. Using the old version I have a single group showing up for each odd residue, eg JJJ shows up once as group 16 for example. When I use the new version on the same file I get 2 groups appearing for residue JJJ and others. Here is the output of that I get from make_ndx. Is there some way I can prevent this? Repeated groups are normal, but certainly undesirable. Since there is nothing functionally wrong with these groups, it's a rather low-priority bug and has been around since Gromacs 4.5 (so several years). The only way to prevent the duplicate groups would be to create an index file that eliminates the duplicates. -Justin 0 System : 126928 atoms 1 Other : 137 atoms 2 NGL : 9 atoms 3 CY1 :10 atoms 4 CAR :25 atoms 5 HEM :73 atoms 6 JJJ : 1 atoms 7 CPZ :19 atoms 8 Cl : 6 atoms 9 Protein : 7475 atoms 10 Protein-H : 3733 atoms 11 C-alpha : 461 atoms 12 Backbone: 1383 atoms 13 MainChain : 1844 atoms 14 MainChain+Cb: 2275 atoms 15 MainChain+H : 2275 atoms 16 SideChain : 5200 atoms 17 SideChain-H : 1889 atoms 18 Prot-Masses : 7475 atoms 19 non-Protein : 119453 atoms 20 Water : 119310 atoms 21 SOL : 119310 atoms 22 non-Water : 7618 atoms 23 Ion : 6 atoms 24 NGL : 9 atoms 25 CY1 :10 atoms 26 CAR :25 atoms 27 HEM :73 atoms 28 JJJ : 1 atoms 29 CPZ :19 atoms 30 Cl : 6 atoms 31 Water_and_ions : 119316 atoms Thanks, - Laura -- 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
Re: [gmx-users] make_ndx select atoms from different residues
On 1/02/2012 5:02 AM, Zhuyi Xue wrote: Hi, there I would like to select, for example, CA of GLY, CB of PRO, so I typed r GLY a CA | r PRO a CB, but it doesn't work. make_ndx also doesn't support parenthesis, either. Previously, I used r GLY a CA (save as group 1), then r PRO a CB (save as group 2), then 1|2, and finally del 1, del 1 to complete my selection, but this is really not ideal! Is there a easier way to do the selection in one step? make_ndx is not as fully featured as one might like. You can probably do this operation in one shot using g_select. Mark I would really appreciate it if anyone could give a hint. Thank you. Zhuyi -- 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_ndx and rdf
Molecular Dynamics wrote: Dear All, I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water using g_rdf but how can I generate an .ndx file that are suitable for these systems ? I searched mailing list and read manual but couldn't generate .ndx file using make_ndx tool. However, I tried to see the make_ndx examples in gromacs wiki page but couldn't reach the wiki page. Could you please help me about generating .ndx file ? Carbon in group 1 hydrogen in group 2 oxygen in group 2 group 2 is water I will be gratefull for your helps. Have you tried typing help at the make_ndx prompt? You'll get tons of information, including the commands needed to create the groups you want. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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_ndx and rdf
Dear Justin, Of course I tried typing help at the make_ndx prompt but I couldn't generate a .ndx file for my purposes. I strongly need expert help for using make_ndx tool. I'm trying to generate .ndx file for more than one week. Finally I decided to ask it to mailing list. So I will be appreciate for any help. Thanks for your help. From: Justin A. Lemkul jalem...@vt.edu To: Molecular Dynamics moleculardynam...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, October 3, 2011 5:17 PM Subject: Re: [gmx-users] make_ndx and rdf Molecular Dynamics wrote: Dear All, I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water using g_rdf but how can I generate an .ndx file that are suitable for these systems ? I searched mailing list and read manual but couldn't generate .ndx file using make_ndx tool. However, I tried to see the make_ndx examples in gromacs wiki page but couldn't reach the wiki page. Could you please help me about generating .ndx file ? Carbon in group 1 hydrogen in group 2 oxygen in group 2 group 2 is water I will be gratefull for your helps. Have you tried typing help at the make_ndx prompt? You'll get tons of information, including the commands needed to create the groups you want. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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-- 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_ndx and rdf
oguz gurbulak wrote: Dear Justin, Of course I tried typing help at the make_ndx prompt but I couldn't generate a .ndx file for my purposes. I strongly need expert help for OK, you didn't say that. You said you tried the mailing list, manual, and the wiki was unavailable. The help prompt is the best option. If you don't state everything you tried, I'm going to go with the remaining option(s) :) using make_ndx tool. I'm trying to generate .ndx file for more than one week. Finally I decided to ask it to mailing list. So I will be appreciate for any help. For example, water oxygens (assuming SOL is group 2, as you said) 2 a OW Water hydrogens 2 a H* All carbon atoms in group 1 1 a C* -Justin Thanks for your help. *From:* Justin A. Lemkul jalem...@vt.edu *To:* Molecular Dynamics moleculardynam...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Monday, October 3, 2011 5:17 PM *Subject:* Re: [gmx-users] make_ndx and rdf Molecular Dynamics wrote: Dear All, I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water using g_rdf but how can I generate an .ndx file that are suitable for these systems ? I searched mailing list and read manual but couldn't generate .ndx file using make_ndx tool. However, I tried to see the make_ndx examples in gromacs wiki page but couldn't reach the wiki page. Could you please help me about generating .ndx file ? Carbon in group 1 hydrogen in group 2 oxygen in group 2 group 2 is water I will be gratefull for your helps. Have you tried typing help at the make_ndx prompt? You'll get tons of information, including the commands needed to create the groups you want. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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_ndx unable to save
ram bio wrote: Dear Gromacs Users, I have simulated a protein -ligand complex in the popc bilayer and while analysing the results i want to find distance between two residues in the protein during simulation. For that I think I have to use g_hbond command by creating an index.file containing the new groups, but while creating the new index file I could select groups , but unable to save them using 'q' command. jhcdyprod31ns.gro is the output file after simulation for a period of time. I executed the command: make_ndx -f jhcdyprod31ns.gro -o output.ndx / *then i got the following options,*/ Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 539Protein residues There are: 5Ion residues There are: 133 Other residues There are: 15828 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 62876 atoms 1 Protein : 8470 atoms 2 Protein-H : 4235 atoms 3 C-alpha : 539 atoms 4 Backbone: 1617 atoms 5 MainChain : 2157 atoms 6 MainChain+Cb: 2652 atoms 7 MainChain+H : 2675 atoms 8 SideChain : 5795 atoms 9 SideChain-H : 2078 atoms 10 Prot-Masses : 8470 atoms 11 non-Protein : 54406 atoms 12 Ion : 5 atoms 13 NA : 2 atoms 14 CL : 1 atoms 15 LIG :53 atoms 16 POPC: 6864 atoms 17 CL- : 2 atoms 18 Other : 6917 atoms 19 NA : 2 atoms 20 CL : 1 atoms 21 LIG :53 atoms 22 POPC: 6864 atoms 23 CL- : 2 atoms 24 Water : 47484 atoms 25 SOL : 47484 atoms 26 non-Water : 15392 atoms 27 Water_and_ions : 47489 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 'ri': residue index * but, i wanted to create a new group, so i selected a residue number 15 and verified it as a new group added in the index file, this was ok * r15 28 r_15:12 atoms* 0 System : 62876 atoms 1 Protein : 8470 atoms 2 Protein-H : 4235 atoms 3 C-alpha : 539 atoms 4 Backbone: 1617 atoms 5 MainChain : 2157 atoms 6 MainChain+Cb: 2652 atoms 7 MainChain+H : 2675 atoms 8 SideChain : 5795 atoms 9 SideChain-H : 2078 atoms 10 Prot-Masses : 8470 atoms 11 non-Protein : 54406 atoms 12 Ion : 5 atoms 13 NA : 2 atoms 14 CL : 1 atoms 15 LIG :53 atoms 16 POPC: 6864 atoms 17 CL- : 2 atoms 18 Other : 6917 atoms 19 NA : 2 atoms 20 CL : 1 atoms 21 LIG :53 atoms 22 POPC: 6864 atoms 23 CL- : 2 atoms 24 Water : 47484 atoms 25 SOL : 47484 atoms 26 non-Water : 15392 atoms 27 Water_and_ions : 47489 atoms 28 r_15:12 atoms then**, i save it with q command * q Back Off! I just backed up output.ndx to ./#output.ndx.15# but, when i wanted to add another group to this index file i again i could not see the first new group added i.e. it has the default groups, the new groups added are not saved. You need to provide your custom index group as input to make_ndx if you want to make use of that group further, e.g.: make_ndx -f jhcdyprod31ns.gro -n output.ndx -o output2.ndx -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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_ndx for do_dssp
Hello, I want to check the secondary structure of protein at particular residues. Since dssp needs all main chain atoms, does the following command at the make_ndx prompt makes the correct index file? 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45 (Main chain atom of particular residues). regards, Paymon -- 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_ndx for do_dssp
Paymon Pirzadeh wrote: Hello, I want to check the secondary structure of protein at particular residues. Since dssp needs all main chain atoms, does the following command at the make_ndx prompt makes the correct index file? You can answer that yourself by looking at the resulting index file. 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45 To get these groups to merge, I think you probably need to do 5 r 1 | ... -Justin (Main chain atom of particular residues). regards, Paymon -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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_ndx for do_dssp
Justin, I produced the index file based on your suggestion, but when I ran the do_dssp, a completely different result was spit out comparing to what the whole protein analysis had given. Any ideas on why that might have happened? Paymon On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Hello, I want to check the secondary structure of protein at particular residues. Since dssp needs all main chain atoms, does the following command at the make_ndx prompt makes the correct index file? You can answer that yourself by looking at the resulting index file. 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45 To get these groups to merge, I think you probably need to do 5 r 1 | ... -Justin (Main chain atom of particular residues). regards, Paymon -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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_ndx for do_dssp
Paymon Pirzadeh wrote: Justin, I produced the index file based on your suggestion, but when I ran the do_dssp, a completely different result was spit out comparing to what the whole protein analysis had given. Any ideas on why that might have happened? That depends on what completely different means. I have no idea. If you're only analyzing a subset of the residues, you're going to get a discontinuous plot that's probably going to look a whole lot different from any analysis done on the whole protein. What's more, if you're only considering small fragments of the protein, then omitting surrounding residues from the analysis probably won't permit DSSP to find hydrogen bonding partners that are necessary to determine the correct secondary structure. -Justin Paymon On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Hello, I want to check the secondary structure of protein at particular residues. Since dssp needs all main chain atoms, does the following command at the make_ndx prompt makes the correct index file? You can answer that yourself by looking at the resulting index file. 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45 To get these groups to merge, I think you probably need to do 5 r 1 | ... -Justin (Main chain atom of particular residues). regards, Paymon -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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_ndx for do_dssp
I assumption was that when provide the index file, do_dssp will do the analysis for the protein but prints out the results only for the designated residues. All I wanted was a better resolution on the final xpm plot to see the secondary structure of the protein at those residues of interest. Any suggestions on how we can increase the resolution of dssp plot and enlarging the axis of residues? By the way, what would the option -nice do here? Paymon On Wed, 2010-10-06 at 15:29 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Justin, I produced the index file based on your suggestion, but when I ran the do_dssp, a completely different result was spit out comparing to what the whole protein analysis had given. Any ideas on why that might have happened? That depends on what completely different means. I have no idea. If you're only analyzing a subset of the residues, you're going to get a discontinuous plot that's probably going to look a whole lot different from any analysis done on the whole protein. What's more, if you're only considering small fragments of the protein, then omitting surrounding residues from the analysis probably won't permit DSSP to find hydrogen bonding partners that are necessary to determine the correct secondary structure. -Justin Paymon On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Hello, I want to check the secondary structure of protein at particular residues. Since dssp needs all main chain atoms, does the following command at the make_ndx prompt makes the correct index file? You can answer that yourself by looking at the resulting index file. 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45 To get these groups to merge, I think you probably need to do 5 r 1 | ... -Justin (Main chain atom of particular residues). regards, Paymon -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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_ndx for do_dssp
Paymon Pirzadeh wrote: I assumption was that when provide the index file, do_dssp will do the analysis for the protein but prints out the results only for the designated residues. All I wanted was a better resolution on the final When prompted for only one group, that group is used for calculation and output. xpm plot to see the secondary structure of the protein at those residues of interest. Any suggestions on how we can increase the resolution of dssp plot and enlarging the axis of residues? Yes, use an .m2p file to adjust the matrix spacing. This was discussed several days ago. By the way, what would the option -nice do here? Likely nothing. Nice levels are irrelevant for most tasks. -Justin Paymon On Wed, 2010-10-06 at 15:29 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Justin, I produced the index file based on your suggestion, but when I ran the do_dssp, a completely different result was spit out comparing to what the whole protein analysis had given. Any ideas on why that might have happened? That depends on what completely different means. I have no idea. If you're only analyzing a subset of the residues, you're going to get a discontinuous plot that's probably going to look a whole lot different from any analysis done on the whole protein. What's more, if you're only considering small fragments of the protein, then omitting surrounding residues from the analysis probably won't permit DSSP to find hydrogen bonding partners that are necessary to determine the correct secondary structure. -Justin Paymon On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Hello, I want to check the secondary structure of protein at particular residues. Since dssp needs all main chain atoms, does the following command at the make_ndx prompt makes the correct index file? You can answer that yourself by looking at the resulting index file. 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45 To get these groups to merge, I think you probably need to do 5 r 1 | ... -Justin (Main chain atom of particular residues). regards, Paymon -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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_ndx: execlude one group from another
Thomas Schlesier skrev 2010-09-23 13.03: Hi all, I'm trying to execlude all atoms of group 2 (140 atoms) from group 1 (300 atoms), so that i have a new group 3 (with 160 atoms). | is for merging with OR for merging with AND so ! should be for merging with NOT But i tried 1 ! 2 2 ! 1 but in both cases make_ndx complains about syntax errors Syntax error: ! 1 ; or same with ! 2 To use NOT instead of ! doesn't work. But using AND insted of also doesn't work. So what's the right command for merging with the NOT option? Greetings Thomas I guess that's because ! is not a binary operator. If you want the union of 1 and all that is not in 2, then try '1 | ! 2'. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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_ndx: execlude one group from another
- Original Message - From: Thomas Schlesier schl...@uni-mainz.de Date: Friday, September 24, 2010 18:43 Subject: [gmx-users] make_ndx: execlude one group from another To: gmx-users@gromacs.org gmx-users@gromacs.org Hi all, I'm trying to execlude all atoms of group 2 (140 atoms) from group 1 (300 atoms), so that i have a new group 3 (with 160 atoms). | is for merging with OR for merging with AND so ! should be for merging with NOT No. NOT is a unary operator, which (in this case) negates the sense of a set. You can be in A or NOT in A. In English we might say in B not A which makes sense (sloppily), but there's an implicit AND binary operator to combine the two operands, viz in B AND NOT in A. make_ndx requires the precise version. Mark But i tried 1 ! 2 2 ! 1 but in both cases make_ndx complains about syntax errors Syntax error: ! 1 ; or same with ! 2 To use NOT instead of ! doesn't work. But using AND insted of also doesn't work. So what's the right command for merging with the NOT option? Greetings Thomas -- 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
Re: [gmx-users] make_ndx help
1|12 merges the two groups into a new group (112 will merge into a new group any atoms which are in both groups 1 and 12, of which there are none in this case) Tom --On Wednesday, August 26, 2009 04:07:20 +0530 parthi...@ncbs.res.in wrote: Hi Anyone can please tell how to index 2 or more groups using make_ndx eg: 1 protein 12 sol 13 NA+ i tried giving 112, which shows that the Group is empty thanks in advance Parthiban ___ 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 -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ 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_ndx help
parthi...@ncbs.res.in wrote: Hi Anyone can please tell how to index 2 or more groups using make_ndx eg: 1 protein 12 sol 13 NA+ i tried giving 112, which shows that the Group is empty Type help at the make_ndx prompt; you will see a number of examples. There are also more examples on the wiki: http://oldwiki.gromacs.org/index.php/make_ndx -Justin thanks in advance Parthiban ___ 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 -- 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
Re: [gmx-users] make_ndx option
Hi Anirban, when you choose in make_ndx, you choose group 3 and () r 2 3 4 5 6...and so on... in make_ndx there is a legend that explain this passage well... Bye! 2009/7/9 Anirban Ghosh anirban...@yahoo.co.in Hi ALL, I want to create an index file using make_ndx which will contain only C-alpha atoms of some residues (like from residue no 2-10, res 25-30, res 36-40). How should I give this option in make_ndx. Any suggestion is welcome. Regards, *Anirban Ghosh* *Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India * -- Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/ . ___ 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 ___ 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_ndx option
Hi Anirban ! First u hav to notedown the C-alpha atoms nos seperately from ur atom file. Then execute the command make_ndx -f input.gro -o index.ndx.After this command, it gives a prompt. At that prompt you have to make a new group for the core region, for this you need to have the list of residues in the core region. So prepare a list of residues that form the core region ready. Suppose your list has residues 10,11,12...,101,102 etc., At the prompt give r10|r11|r12|.so on and press enter. You can rename the newly formed group by giving command, name group number new_name On Thu, Jul 9, 2009 at 3:38 PM, Anirban Ghosh anirban...@yahoo.co.inwrote: Hi ALL, I want to create an index file using make_ndx which will contain only C-alpha atoms of some residues (like from residue no 2-10, res 25-30, res 36-40). How should I give this option in make_ndx. Any suggestion is welcome. Regards, *Anirban Ghosh* *Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India * -- Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/ . ___ 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 -- With Best Wishes Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ 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: Re: [gmx-users] make_ndx option
Hi, Use splitat for group 3. sharada -- Original Message -- From: Venkat Reddy venkat...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thu, 9 Jul 2009 19:54:18 +0530 Subject: Re: [gmx-users] make_ndx option Hi Anirban ! First u hav to notedown the C-alpha atoms nos seperately from ur atom file. Then execute the command make_ndx -f input.gro -o index.ndx.After this command, it gives a prompt. At that prompt you have to make a new group for the core region, for this you need to have the list of residues in the core region. So prepare a list of residues that form the core region ready. Suppose your list has residues 10,11,12...,101,102 etc., At the prompt give r10|r11|r12|.so on and press enter. You can rename the newly formed group by giving command, name group number new_name On Thu, Jul 9, 2009 at 3:38 PM, Anirban Ghosh anirban...@yahoo.co.inanirban...@yahoo.co.in wrote: Hi ALL, I want to create an index file using make_ndx which will contain only C-alpha atoms of some residues (like from residue no 2-10, res 25-30, res 36-40). How should I give this option in make_ndx. Any suggestion is welcome. Regards, Anirban Ghosh Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India Internet Explorer 8. ___ gmx-users mailing list gmx-users@gromacs.orggmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/searchhttp://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.orggmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.phphttp://www.gromacs.org/mailing_lists/users.php -- With Best Wishes Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ 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/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___ 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: Re: Re: [gmx-users] make_ndx problem
I think, after creating an index file, you can edit it manually clubbing both Phosphorius and Oxygen atoms together ( considering as a single group). Then specify this group while doing analysis. On Wed, 16 Jul 2008 minnale wrote : Thanks for the reply, may be this is trivial question to you That I know that how to select phosrous atom alone of POPC. Normally people are using only phosphrous atom or PO4 group ? for density calculation ,etc analysis. In one article I found that they have done density analysis for PO4 group. Could you please tell me which one use it for analysis if PO4 how select by using make_ndx? Thanks alot in advance. ___ 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] make_ndx problem
Hi, On Wednesday, 16. July 2008, minnale wrote: Hi Users, I want to do analysis of g_density of lipidbilayer so how can I select po4 and N(CH3)3 groups seperately by using make_ndx from popc. Can anyone tell me detail with which options use? I have checked in archives that create sn1.ndx and sn2.ndx files but i didnt get celarly. Thanks in advance Take first a look on your .gro file and identify the atoms you want to select. try something like: make_ndx -f your_file.gro a P* this should select all atoms with P in your system., it also depends on the used force field. Also h prints out some inforamation about the selection choices. greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ 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: Re: [gmx-users] make_ndx problem
Thanks for the reply, may be this is trivial question to you That I know that how to select phosrous atom alone of POPC. Normally people are using only phosphrous atom or PO4 group ? for density calculation ,etc analysis. In one article I found that they have done density analysis for PO4 group. Could you please tell me which one use it for analysis if PO4 how select by using make_ndx? Thanks alot in advance. On Wed, 16 Jul 2008 Florian Haberl wrote : Hi, On Wednesday, 16. July 2008, minnale wrote: Hi Users, I want to do analysis of g_density of lipidbilayer so how can I select po4 and N(CH3)3 groups seperately by using make_ndx from popc. Can anyone tell me detail with which options use? I have checked in archives that create sn1.ndx and sn2.ndx files but i didnt get celarly. Thanks in advance Take first a look on your .gro file and identify the atoms you want to select. try something like: make_ndx -f your_file.gro a P* this should select all atoms with P in your system., it also depends on the used force field. Also h prints out some inforamation about the selection choices. greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) â 9131 â 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ 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] make_ndx problem
minnale wrote: Thanks for the reply, may be this is trivial question to you That I know that how to select phosrous atom alone of POPC. Normally people are using only phosphrous atom or PO4 group ? for density calculation ,etc analysis. In one article I found that they have done density analysis for PO4 group. Could you please tell me which one use it for analysis if PO4 how select by using make_ndx? Thanks alot in advance. I have seen both P and PO4 analyzed, as well. It's up to you to decide what is most relevant for your situation. I updated the wiki page this morning to include some examples: http://wiki.gromacs.org/index.php/make_ndx -Justin On Wed, 16 Jul 2008 Florian Haberl wrote : Hi, On Wednesday, 16. July 2008, minnale wrote: Hi Users, I want to do analysis of g_density of lipidbilayer so how can I select po4 and N(CH3)3 groups seperately by using make_ndx from popc. Can anyone tell me detail with which options use? I have checked in archives that create sn1.ndx and sn2.ndx files but i didnt get celarly. Thanks in advance Take first a look on your .gro file and identify the atoms you want to select. try something like: make_ndx -f your_file.gro a P* this should select all atoms with P in your system., it also depends on the used force field. Also h prints out some inforamation about the selection choices. greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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] make_ndx problem
minnale wrote: but here I am calculating density for 128 lipids not for 64 lipids. Is it right what iam doing? The examples on the wiki are just a few illustrative ideas, meant to inspire the fact that you can analyze whatever subset of your system you wish. You can certainly analyze all headgroups at once. The point was that, if, for example, you have a small molecule or protein (or whatever else) interacting with the surface of one leaflet of the bilayer, you may wish to divide your structure into different subsets. -Justin On Wed, 16 Jul 2008 Justin A.Lemkul wrote : minnale wrote: Thanks for the reply, may be this is trivial question to you That I know that how to select phosrous atom alone of POPC. Normally people are using only phosphrous atom or PO4 group ? for density calculation ,etc analysis. In one article I found that they have done density analysis for PO4 group. Could you please tell me which one use it for analysis if PO4 how select by using make_ndx? Thanks alot in advance. I have seen both P and PO4 analyzed, as well. It's up to you to decide what is most relevant for your situation. I updated the wiki page this morning to include some examples: http://wiki.gromacs.org/index.php/make_ndx -Justin On Wed, 16 Jul 2008 Florian Haberl wrote : Hi, On Wednesday, 16. July 2008, minnale wrote: Hi Users, I want to do analysis of g_density of lipidbilayer so how can I select po4 and N(CH3)3 groups seperately by using make_ndx from popc. Can anyone tell me detail with which options use? I have checked in archives that create sn1.ndx and sn2.ndx files but i didnt get celarly. Thanks in advance Take first a look on your .gro file and identify the atoms you want to select. try something like: make_ndx -f your_file.gro a P* this should select all atoms with P in your system., it also depends on the used force field. Also h prints out some inforamation about the selection choices. greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null -- Justin A. Lemkul Graduate Research Assistant 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://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: Re: [gmx-users] make_ndx problem
Thanks once again. Ideally I shouldnt do for whole system. Ok. On Wed, 16 Jul 2008 Justin A.Lemkul wrote : minnale wrote: but here I am calculating density for 128 lipids not for 64 lipids. Is it right what iam doing? The examples on the wiki are just a few illustrative ideas, meant to inspire the fact that you can analyze whatever subset of your system you wish. You can certainly analyze all headgroups at once. The point was that, if, for example, you have a small molecule or protein (or whatever else) interacting with the surface of one leaflet of the bilayer, you may wish to divide your structure into different subsets. -Justin On Wed, 16 Jul 2008 Justin A.Lemkul wrote : minnale wrote: Thanks for the reply, may be this is trivial question to you That I know that how to select phosrous atom alone of POPC. Normally people are using only phosphrous atom or PO4 group ? for density calculation ,etc analysis. In one article I found that they have done density analysis for PO4 group. Could you please tell me which one use it for analysis if PO4 how select by using make_ndx? Thanks alot in advance. I have seen both P and PO4 analyzed, as well. It's up to you to decide what is most relevant for your situation. I updated the wiki page this morning to include some examples: http://wiki.gromacs.org/index.php/make_ndx -Justin On Wed, 16 Jul 2008 Florian Haberl wrote : Hi, On Wednesday, 16. July 2008, minnale wrote: Hi Users, I want to do analysis of g_density of lipidbilayer so how can I select po4 and N(CH3)3 groups seperately by using make_ndx from popc. Can anyone tell me detail with which options use? I have checked in archives that create sn1.ndx and sn2.ndx files but i didnt get celarly. Thanks in advance Take first a look on your .gro file and identify the atoms you want to select. try something like: make_ndx -f your_file.gro a P* this should select all atoms with P in your system., it also depends on the used force field. Also h prints out some inforamation about the selection choices. greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) â 9131 â 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null -- Justin A. Lemkul Graduate Research Assistant 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://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] make_ndx problem
On 7 May 2008 07:10:11 - minnale [EMAIL PROTECTED] wrote: Hi all, it may be trivial question My protien contain nearly 200 residues, I want plot RMSD for 45 to 90 residues , So I made make_ndx file also, but I am doubting that what i have I done whether right ot wrong? I have selcted 1 | r 45-90 1 = protein , the way I have selected is correct or I have to select 3 | r 45-90 3 = C-alpha This won't give you what you want. you have to use 1 r 45-90 : all protein atoms whithin residues 45-90 or 3 45-90 : all Ca atoms within residue 45-90 the sign | adds up the two groups the sign take the intersection between the groups you could do the check yourself, by editing the output index it and verify that the atom numbers given are or not what you want. Pls tell me Thanks in advance - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ 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] make_ndx
sarbani chattopadhyay wrote: hi, I want to select two groups in the index file, one group consisting of only the aromatic ring of phenylalanine and the other group consisting of only the alpha carbon. I want to know the way to use the make_ndx command for this. After entering make_ndx, you can use hRETURN to get some primitive help. In this case, you can most quickly solve your problem by hand-editing. See http://wiki.gromacs.org/index.php/Index_File 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
Re: Re: [gmx-users] make_ndx
Thanks Mark, I could do it following your suggestion. Sarbani On Wed, 24 Oct 2007 Mark Abraham wrote : sarbani chattopadhyay wrote: hi, I want to select two groups in the index file, one group consisting of only the aromatic ring of phenylalanine and the other group consisting of only the alpha carbon. I want to know the way to use the make_ndx command for this. After entering make_ndx, you can use hRETURN to get some primitive help. In this case, you can most quickly solve your problem by hand-editing. See http:// wiki.gromacs.org/index.php/Index_File 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 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] make_ndx
Hi XAvier, Single out I mean pick up only the side chain bonded with alpha carbon atom and put them in a group using make_ndx. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Wed 26/09/2007 8:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx On Wed, 26 Sep 2007 20:08:06 +0100 Naser, Md Abu [EMAIL PROTECTED] wrote: Hi All User, Is there anyway I can single out side chain of alpha carbon atom using make_ndx? What do you mean by single out and with side chain of alpha carbon ? Thanks in advance. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ 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 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] make_ndx
Naser, Md Abu wrote: Hi XAvier, Single out I mean pick up only the side chain bonded with alpha carbon atom and put them in a group using make_ndx. all side chains are. and sidechain is a default group. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Wed 26/09/2007 8:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx On Wed, 26 Sep 2007 20:08:06 +0100 Naser, Md Abu [EMAIL PROTECTED] wrote: Hi All User, Is there anyway I can single out side chain of alpha carbon atom using make_ndx? What do you mean by single out and with side chain of alpha carbon ? Thanks in advance. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ 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 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] make_ndx
Thanks david! Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Thu 27/09/2007 7:17 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx Naser, Md Abu wrote: Hi XAvier, Single out I mean pick up only the side chain bonded with alpha carbon atom and put them in a group using make_ndx. all side chains are. and sidechain is a default group. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Wed 26/09/2007 8:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx On Wed, 26 Sep 2007 20:08:06 +0100 Naser, Md Abu [EMAIL PROTECTED] wrote: Hi All User, Is there anyway I can single out side chain of alpha carbon atom using make_ndx? What do you mean by single out and with side chain of alpha carbon ? Thanks in advance. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ 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 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 ___ 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] make_ndx
On Thu, 27 Sep 2007 07:08:00 +0100 Naser, Md Abu [EMAIL PROTECTED] wrote: Hi XAvier, Single out I mean pick up only the side chain bonded with alpha carbon atom and put them in a group using make_ndx. What about joining the groups C-alpha and SideChain using: X | Y ; where X and Y are the numbers corresponding to the groups. Note that the C-beta is not included in the sidechain group. you can add them by using something like: a CB; which will create a new group. This should be enough for you to get what you like. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Wed 26/09/2007 8:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx On Wed, 26 Sep 2007 20:08:06 +0100 Naser, Md Abu [EMAIL PROTECTED] wrote: Hi All User, Is there anyway I can single out side chain of alpha carbon atom using make_ndx? What do you mean by single out and with side chain of alpha carbon ? Thanks in advance. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ 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 - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ 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] make_ndx
Naser, Md Abu wrote: Thanks david! oops I misread. Sidechains do not contain C-alpha (which you can easily check in the index file). So within make_ndx type h for help on joining the two. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Thu 27/09/2007 7:17 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx Naser, Md Abu wrote: Hi XAvier, Single out I mean pick up only the side chain bonded with alpha carbon atom and put them in a group using make_ndx. all side chains are. and sidechain is a default group. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Wed 26/09/2007 8:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx On Wed, 26 Sep 2007 20:08:06 +0100 Naser, Md Abu [EMAIL PROTECTED] wrote: Hi All User, Is there anyway I can single out side chain of alpha carbon atom using make_ndx? What do you mean by single out and with side chain of alpha carbon ? Thanks in advance. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ 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 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 ___ 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
RE: [gmx-users] make_ndx
Thanks XAvier and David! I think I know what I need to do to get my group. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Thu 27/09/2007 7:29 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx Naser, Md Abu wrote: Thanks david! oops I misread. Sidechains do not contain C-alpha (which you can easily check in the index file). So within make_ndx type h for help on joining the two. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Thu 27/09/2007 7:17 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx Naser, Md Abu wrote: Hi XAvier, Single out I mean pick up only the side chain bonded with alpha carbon atom and put them in a group using make_ndx. all side chains are. and sidechain is a default group. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Wed 26/09/2007 8:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx On Wed, 26 Sep 2007 20:08:06 +0100 Naser, Md Abu [EMAIL PROTECTED] wrote: Hi All User, Is there anyway I can single out side chain of alpha carbon atom using make_ndx? What do you mean by single out and with side chain of alpha carbon ? Thanks in advance. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ 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 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 ___ 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
Re: [gmx-users] make_ndx
On Wed, 26 Sep 2007 20:08:06 +0100 Naser, Md Abu [EMAIL PROTECTED] wrote: Hi All User, Is there anyway I can single out side chain of alpha carbon atom using make_ndx? What do you mean by single out and with side chain of alpha carbon ? Thanks in advance. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ 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] make_ndx and residue name length
From: Alan Dodd [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] make_ndx and residue name length Date: Tue, 4 Sep 2007 10:55:07 -0700 (PDT) The maximum permissible residue name length is at least 5 characters long for a tpr or gro, but the length of residue name permitted by make_ndx is only 4 characters. And of course, pdb should have only 3 characters. While I can change the names in a gro or a pdb quite quickly and easily, is there a way to change this in a tpr? I'm currently getting around the problem by converting tprs to pdbs for use by make_ndx, but it's messy... Alternatively, is there any fundamental reason why the string in make_ndx inputs is less than that for files, or can I safely bump up the relevant digit in the code and recompile? I did not know about this check, but now that I have looked at the code it seems I have programmed it myself a decade ago. The only reason for a limit was/is programming convenience. You can change it and recompile, but be careful that the number 5 occurs at multiple places in make_ndx.c I was too lazy to remove the limit, so I have set it to 30 now in the CVS (and also put defined this number in one place only). Berk. _ Live Search, for accurate results! http://www.live.nl ___ 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] make_ndx and residue name length
Thanks... I think I'll just get the CVS make_ndx and integrate that into my current CVS copy, rather than try to hunt the different locations down! - Original Message From: Berk Hess [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, September 5, 2007 11:22:15 AM Subject: RE: [gmx-users] make_ndx and residue name length From: Alan Dodd [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] make_ndx and residue name length Date: Tue, 4 Sep 2007 10:55:07 -0700 (PDT) The maximum permissible residue name length is at least 5 characters long for a tpr or gro, but the length of residue name permitted by make_ndx is only 4 characters. And of course, pdb should have only 3 characters. While I can change the names in a gro or a pdb quite quickly and easily, is there a way to change this in a tpr? I'm currently getting around the problem by converting tprs to pdbs for use by make_ndx, but it's messy... Alternatively, is there any fundamental reason why the string in make_ndx inputs is less than that for files, or can I safely bump up the relevant digit in the code and recompile? I did not know about this check, but now that I have looked at the code it seems I have programmed it myself a decade ago. The only reason for a limit was/is programming convenience. You can change it and recompile, but be careful that the number 5 occurs at multiple places in make_ndx.c I was too lazy to remove the limit, so I have set it to 30 now in the CVS (and also put defined this number in one place only). Berk. _ Live Search, for accurate results! http://www.live.nl ___ 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 Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ 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] make_ndx not working
Camilo, What is missing here? Why does make_ndx not see the individual atoms in the configuration file? What is displayed by make_ndx when you have execute it? Which particular file do you run it on? Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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
Re: [gmx-users] make_ndx
Hello Dongsheng! Am Samstag, den 24.06.2006, 17:26 -0400 schrieb Dongsheng Zhang: In make_ndx, I would like to keep two groups, for instance, group 4 and group 5. I have try it in two ways, namely, keep 4 keep 5 and keep 4 | keep 5. However both ways only keep group 4. Anyway to accomplish my task is to delete other groups one by one, but it is not so convenient. Could anyone tell me what is the trick? Thanks! I don't think this can be done directly. Nevertheless, a quite simple solution is to first copy the selections you would like to keep (by just giving the number of the group you want to copy) and then deleting all default groups (del 0-13). Your session might look like this: 4 [Enter] Copied index group 4 'Backbone' 14 Backbone:39 atoms 5 [Enter] Copied index group 5 'MainChain' 15 MainChain :53 atoms del 0-13 [Enter] Removed group 0 'System' Removed group 1 'Protein' Removed group 2 'Protein-H' Removed group 3 'C-alpha' Removed group 4 'Backbone' Removed group 5 'MainChain' Removed group 6 'MainChain+Cb' Removed group 7 'MainChain+H' Removed group 8 'SideChain' Removed group 9 'SideChain-H' Removed group 10 'Prot-Masses' Removed group 11 'Non-Protein' Removed group 12 'SOL' Removed group 13 'Other' [Enter] 0 Backbone:39 atoms 1 MainChain :53 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit q [Enter] The resulting index.ndx contains the desired groups. HTH Manuel ___ 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
Re: [gmx-users] make_ndx
Hello, Manuel, Thank you very much for your trick. It is neat. Have a nice weekend! Dongsheng On Sun, 2006-06-25 at 02:58 +0200, Manuel Prinz wrote: Hello Dongsheng! Am Samstag, den 24.06.2006, 17:26 -0400 schrieb Dongsheng Zhang: In make_ndx, I would like to keep two groups, for instance, group 4 and group 5. I have try it in two ways, namely, keep 4 keep 5 and keep 4 | keep 5. However both ways only keep group 4. Anyway to accomplish my task is to delete other groups one by one, but it is not so convenient. Could anyone tell me what is the trick? Thanks! I don't think this can be done directly. Nevertheless, a quite simple solution is to first copy the selections you would like to keep (by just giving the number of the group you want to copy) and then deleting all default groups (del 0-13). Your session might look like this: 4 [Enter] Copied index group 4 'Backbone' 14 Backbone:39 atoms 5 [Enter] Copied index group 5 'MainChain' 15 MainChain :53 atoms del 0-13 [Enter] Removed group 0 'System' Removed group 1 'Protein' Removed group 2 'Protein-H' Removed group 3 'C-alpha' Removed group 4 'Backbone' Removed group 5 'MainChain' Removed group 6 'MainChain+Cb' Removed group 7 'MainChain+H' Removed group 8 'SideChain' Removed group 9 'SideChain-H' Removed group 10 'Prot-Masses' Removed group 11 'Non-Protein' Removed group 12 'SOL' Removed group 13 'Other' [Enter] 0 Backbone:39 atoms 1 MainChain :53 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit q [Enter] The resulting index.ndx contains the desired groups. HTH Manuel ___ 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 ___ 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
Re: [gmx-users] make_ndx problem
bharat v. adkar wrote: Dear GMX users... i have a protein-peptide complex wherein peptide does not have one of the terminal carboxy oxygen atoms (i.e., it has -CO only). I designate A to peptide and B to protein chain. when i do pdb2gmx, it adds the missing O, so now the group is -COO. Now with this gro file, i tried to make some groups with make_ndx. when i select group 0 (system) or 1 (protein), and try to generate index file, i get the following error... *** glibc detected *** double free or corruption: 0x081b5bc0 *** Aborted if this is reproducible then please file a bugzilla. but when i use any other groups to make some index file, i do not get any error Moreover, when i solvate the system, and use the resultant gro in make_ndx, i get no errors with any combination of groups!!! i am really confused please help... bharat ___ 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 -- 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 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
