[gmx-users] Orders of the residues in gromacs
On 3/02/2012 7:26 PM, Du Jiangfeng (BIOCH) wrote: Dear Justin and Jiangguo, It's still the issue about residue numbering. Actually, the gromacs version is 4.5.3, and I am using Martini coarse grained simulation, where I presume that gromacs reads residues from .gro file randomly, because there are no residues fetched correctly when I picked a list of residues for testing. Plus, I didn't use pdb2gmx program. In my gro file, it contains protein, lipids, ion, and water. :( :( :( :( :( :( Residue numbering is not random - there's a rule that you don't understand, and that's quite a different thing :-) If you are interested in learning how to manage the rule, then there are better ways to approach your search for knowledge than to suggest that people providing you with free tools have gone out of their way to make their use frustrating! :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Orders of the residues in gromacs
Hi, You are probably mixing "resid" and "residue". In VMD, - "resid" is taken as found in the file (pdb, gro, etc). You may have several residues with the same "resid" if you load a file with multiple chains. - "residue" is generated internally by VMD, it is incremented by one unit for each residue, even if there are gaps in the sequence, it always starts at 0 and is granted to be unique for each residue. Cheers, Rui Rodrigues De: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] Em Nome De Du Jiangfeng (BIOCH) [j...@maastrichtuniversity.nl] Enviado: sexta-feira, 3 de Fevereiro de 2012 9:06 Para: gmx-users@gromacs.org Assunto: [gmx-users] RE: gmx-users Digest, Vol 94, Issue 24 Dear All, I found a strange thing about VMD. When I use mouse label residue from graph (Mouse --> Label --> Atom), i would get a correct residue as it is in .gro file, while when I use graphics --> representations --> selections, then the residue selected here is totally different with the one which has the same number in the .gro file. Be careful with it, everybody. Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands Dear Friends, I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem. The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( --> r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file. Does anybody know how to link the gromacs order to the structure file's order correctly? Thank you in advance, Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands -- Message: 4 Date: Thu, 02 Feb 2012 12:43:17 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Orders of the residues in gromacs To: Discussion list for GROMACS users Message-ID: <4f2acb35.8050...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Du Jiangfeng (BIOCH) wrote: > Dear Friends, > > I want to measure some data of a special residue, for instance TRP143, from > my MD result. But i encountered a problem. > > The residue number 143 is ordered in .gro file, while it seems the residue > orders is random in gromacs. It points to another residue when I specify > residue number 143 in VMD or when I am using make_ndx program ( --> r 143; > q). Apparently, gromacs numbering system is not based on the orders in the > .gro structure file. > > Does anybody know how to link the gromacs order to the structure file's order > correctly? > Depending on the Gromacs version you're using, residue numbering is treated differently. In pdb2gmx, you can choose to renumber the residues from 1 or not. The default is to not renumber the file. You should check to see what you did with respect to this option and whether or not your coordinate file is numbered from 1. If it is not, then what you think is residue 143 may not be interpreted that way by all external programs, depending on whether or not they respect the numbering of the .gro file. -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 ============ ---------- Message: 8 Date: Fri, 3 Feb 2012 10:04:28 +0800 (SGT) From: Jianguo Li Subject: Re: [gmx-users] Orders of the residues in gromacs To: Discussion list for GROMACS users Message-ID: <1328234668.1600.yahoomail...@web190204.mail.sg3.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Another possible reason is due to vmd, which numbers the residue from 0. Residue 143 in gromacs corresponds to residue 142 in vmd. Cheers, Jianguo -- 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] Orders of the residues in gromacs
Another possible reason is due to vmd, which numbers the residue from 0. Residue 143 in gromacs corresponds to residue 142 in vmd. Cheers, Jianguo From: Du Jiangfeng (BIOCH) To: "gmx-users@gromacs.org" Sent: Friday, 3 February 2012, 1:16 Subject: [gmx-users] Orders of the residues in gromacs Dear Friends, I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem. The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( --> r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file. Does anybody know how to link the gromacs order to the structure file's order correctly? Thank you in advance, Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands-- 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] Orders of the residues in gromacs
Du Jiangfeng (BIOCH) wrote: Dear Friends, I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem. The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( --> r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file. Does anybody know how to link the gromacs order to the structure file's order correctly? Depending on the Gromacs version you're using, residue numbering is treated differently. In pdb2gmx, you can choose to renumber the residues from 1 or not. The default is to not renumber the file. You should check to see what you did with respect to this option and whether or not your coordinate file is numbered from 1. If it is not, then what you think is residue 143 may not be interpreted that way by all external programs, depending on whether or not they respect the numbering of the .gro file. -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
[gmx-users] Orders of the residues in gromacs
Dear Friends, I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem. The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( --> r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file. Does anybody know how to link the gromacs order to the structure file's order correctly? Thank you in advance, Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands-- 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
