Re: [gmx-users] Make index command in gromacs
Dear Gromacs Users, Thank you very much for your valuable answers. On Wed, Jan 8, 2020 at 8:40 PM Christian Blau wrote: > Hi Shan, > > > gmx select gives you many more options to do complex arithmetic with > selections that might help you here. > > > You can try using > > gmx select -select "SELECTION STING" > > you'll find lots of selection string examples at the bottom in here: > > http://manual.gromacs.org/documentation/current/onlinehelp/selections.html > > > > Best, > > Christian > > > On 2020-01-07 23:33, Shan Jayasinghe wrote: > > Dear Gromacs Users, > > > > In my simulations, I have different sizes of water droplets. I need > > indexes of water molecules in each droplet separately. I am trying to > make > > the index file with gmx make_ndx, but I couldn't do it. Appreciate your > > help regarding this matter. > > > > Thank you. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Best Regards Shan Jayasinghe -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Make index command in gromacs
Hi Shan, gmx select gives you many more options to do complex arithmetic with selections that might help you here. You can try using gmx select -select "SELECTION STING" you'll find lots of selection string examples at the bottom in here: http://manual.gromacs.org/documentation/current/onlinehelp/selections.html Best, Christian On 2020-01-07 23:33, Shan Jayasinghe wrote: Dear Gromacs Users, In my simulations, I have different sizes of water droplets. I need indexes of water molecules in each droplet separately. I am trying to make the index file with gmx make_ndx, but I couldn't do it. Appreciate your help regarding this matter. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Make index command in gromacs
Hi, Maybe you could use gmx select to generate your index file http://manual.gromacs.org/documentation/current/onlinehelp/gmx-select.html?highlight=select Best regards Alessandra On Tue, Jan 7, 2020 at 11:39 PM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Dear Gromacs Users, > > In my simulations, I have different sizes of water droplets. I need > indexes of water molecules in each droplet separately. I am trying to make > the index file with gmx make_ndx, but I couldn't do it. Appreciate your > help regarding this matter. > > Thank you. > -- > Best Regards > Shan Jayasinghe > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Make index command in gromacs
Dear Gromacs Users, In my simulations, I have different sizes of water droplets. I need indexes of water molecules in each droplet separately. I am trying to make the index file with gmx make_ndx, but I couldn't do it. Appreciate your help regarding this matter. Thank you. -- Best Regards Shan Jayasinghe -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] make index for protein multiple ligand md simulation
It should be Protein_index_number | ligand_index_number | cofactor_index_number (In a single line) and you are done!!! On Sun, 14 Apr 2019, 4:14 am m mar, wrote: > dear users > I want to run md simulation for protein with cofactor and ligand > simultaneously, but I dont know how I should merge protein and ligands > together in make index step . > thanks for your help > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] make index for protein multiple ligand md simulation
dear users I want to run md simulation for protein with cofactor and ligand simultaneously, but I dont know how I should merge protein and ligands together in make index step . thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] make index
On 7/23/18 8:42 AM, farial tavakoli wrote: Dear GMX users I am trying to make an index.ndx file of my complex which includes a receptor and a peptide using this command: gmx make_ndx -f em.gro -o index.ndx Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 330 Protein residues There are: 15278 Water residues There are: 7 Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 51172 atoms 1 Protein : 5331 atoms 2 Protein-H : 2659 atoms 3 C-alpha : 330 atoms 4 Backbone : 990 atoms 5 MainChain : 1322 atoms 6 MainChain+Cb : 1633 atoms 7 MainChain+H : 1639 atoms 8 SideChain : 3692 atoms 9 SideChain-H : 1337 atoms 10 Prot-Masses : 5331 atoms 11 non-Protein : 45841 atoms 12 Water : 45834 atoms 13 SOL : 45834 atoms 14 non-Water : 5338 atoms 15 Ion : 7 atoms 16 NA : 7 atoms 17 Water_and_ions : 45841 atoms nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index splitch 1 Found 10 chains 1: 189 atoms (1 to 189) 2: 108 atoms (190 to 297) 3: 283 atoms (298 to 580) 4: 130 atoms (581 to 710) 5: 173 atoms (711 to 883) 6: 10 atoms (884 to 893) 7: 4087 atoms (894 to 4980) 8: 99 atoms (4981 to 5079) 9: 125 atoms (5080 to 5204) 10: 127 atoms (5205 to 5331) I dont know it found 10 chains instead of finding 2 chains ( chain A and chain B).How can I make the desired index file composed of:18 protein chain A19 protein chain B You need to use an input file format that includes chain information, like .pdb or .tpr - there is no chain information in a .gro file. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] make index
Dear GMX users I am trying to make an index.ndx file of my complex which includes a receptor and a peptide using this command: gmx make_ndx -f em.gro -o index.ndx Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 330 Protein residues There are: 15278 Water residues There are: 7 Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 51172 atoms 1 Protein : 5331 atoms 2 Protein-H : 2659 atoms 3 C-alpha : 330 atoms 4 Backbone : 990 atoms 5 MainChain : 1322 atoms 6 MainChain+Cb : 1633 atoms 7 MainChain+H : 1639 atoms 8 SideChain : 3692 atoms 9 SideChain-H : 1337 atoms 10 Prot-Masses : 5331 atoms 11 non-Protein : 45841 atoms 12 Water : 45834 atoms 13 SOL : 45834 atoms 14 non-Water : 5338 atoms 15 Ion : 7 atoms 16 NA : 7 atoms 17 Water_and_ions : 45841 atoms nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index > splitch 1 Found 10 chains 1: 189 atoms (1 to 189) 2: 108 atoms (190 to 297) 3: 283 atoms (298 to 580) 4: 130 atoms (581 to 710) 5: 173 atoms (711 to 883) 6: 10 atoms (884 to 893) 7: 4087 atoms (894 to 4980) 8: 99 atoms (4981 to 5079) 9: 125 atoms (5080 to 5204) 10: 127 atoms (5205 to 5331) I dont know it found 10 chains instead of finding 2 chains ( chain A and chain B).How can I make the desired index file composed of:18 protein chain A19 protein chain B best regardsFarial -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
