Really thank you so much for your reply. can i select the two chain at a time.because both protein contain 120 amino acid respectively. then > ri 1-120
Found 262 atoms with resind.+1 in range 1-120 15 r_1-120 : 262 atoms > rename Chain_A Found 0 atoms with residue names ENAME CHAIN_A Group is empty On 5/24/18, Soham Sarkar <soham9...@gmail.com> wrote: > You should give like ri 1-120 > > On Thu, 24 May 2018, 11:14 am SHAHEE ISLAM, <islamsha...@gmail.com> wrote: > >> yes its working. >> now >> >ri ( give numbers for residue number of each chain) >> i have 120 amino acids of two protein each. >> when i am giving >> > ri 120 >> >> >> 15 r_120 : 2 atoms >> should i give this in the way. >> >> On 5/24/18, Soham Sarkar <soham9...@gmail.com> wrote: >> > Put L(small) >> > It will give the residue number >> > >> > On Thu, 24 May 2018, 11:00 am SHAHEE ISLAM, <islamsha...@gmail.com> >> wrote: >> > >> >> after giving this command >> >> make_ndx -f em.gro -o index.ndx >> >> nr : group ! 'name' nr name 'splitch' nr Enter: 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 >> >> these all options are shown on the screen. >> >> but when i am giving >> >> > | >> >> >> >> >> >> Syntax error: "|" >> >> can you please tell me what should i give. >> >> >> >> >> >> >> >> >> >> On 5/24/18, Soham Sarkar <soham9...@gmail.com> wrote: >> >> > It is any .gro file of your system >> >> > You can make index file after final md >> >> > >> >> > On Thu, 24 May 2018, 10:37 am SHAHEE ISLAM, <islamsha...@gmail.com> >> >> wrote: >> >> > >> >> >> you have mention here em.gro,i think it is a gro file of >> >> >> equilibration.can i make the index file after production run to >> >> >> calculate rmsd. >> >> >> >> >> >> On 5/23/18, SHAHEE ISLAM <islamsha...@gmail.com> wrote: >> >> >> > thank you so much for your quick reply. >> >> >> > >> >> >> > On 5/23/18, Soham Sarkar <soham9...@gmail.com> wrote: >> >> >> >> Do proper indexing of each chain >> >> >> >>> make_ndx -f em.gro -o index.ndx >> >> >> >>>l (shows total residue with number) >> >> >> >>>ri ( give numbers for residue number of each chain) >> >> >> >>>rename them as Chain_A and Chain_B >> >> >> >>>v (shows the newly indexed file) >> >> >> >>>q (save) >> >> >> >> Now your index has two chain seperated >> >> >> >> >> >> >> >> On Wed, May 23, 2018 at 5:54 PM, SHAHEE ISLAM >> >> >> >> <islamsha...@gmail.com >> >> > >> >> >> >> wrote: >> >> >> >> >> >> >> >>> hi, >> >> >> >>> i have two protein in my gro file.when i am calculating rmsd by >> >> >> >>> this >> >> >> >>> command >> >> >> >>> g_rms -s dynamic.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns >> >> >> >>> this options are coming >> >> >> >>> Group 0 ( System) has 12059 elements >> >> >> >>> Group 1 ( Protein) has 566 elements >> >> >> >>> Group 2 ( Protein-H) has 566 elements >> >> >> >>> Group 3 ( C-alpha) has 0 elements >> >> >> >>> Group 4 ( Backbone) has 0 elements >> >> >> >>> Group 5 ( MainChain) has 0 elements >> >> >> >>> Group 6 ( MainChain+Cb) has 0 elements >> >> >> >>> Group 7 ( MainChain+H) has 0 elements >> >> >> >>> Group 8 ( SideChain) has 566 elements >> >> >> >>> Group 9 ( SideChain-H) has 566 elements >> >> >> >>> Group 10 ( Prot-Masses) has 566 elements >> >> >> >>> Group 11 ( non-Protein) has 11493 elements >> >> >> >>> Group 12 ( Other) has 11493 elements >> >> >> >>> Group 13 ( W) has 11477 elements >> >> >> >>> Group 14 ( ION) has 16 elements >> >> >> >>> for this reason i am able to calculate the rmsd of two protein >> >> >> >>> together by selecting 1. >> >> >> >>> but i want to calculate the rmsd of the protein individualy.how >> >> >> >>> i >> >> >> >>> will >> >> >> >>> do >> >> >> >>> this. >> >> >> >>> My .gro file consist of atom no 1 to 283 for protein1 and atom >> >> >> >>> no >> >> 284 >> >> >> >>> to 566 for protein2. >> >> >> >>> thanking you >> >> >> >>> shahee islam >> >> >> >>> university of calcutta >> >> >> >>> -- >> >> >> >>> Gromacs Users mailing list >> >> >> >>> >> >> >> >>> * Please search the archive at http://www.gromacs.org/ >> >> >> >>> Support/Mailing_Lists/GMX-Users_List before posting! >> >> >> >>> >> >> >> >>> * Can't post? 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