Ok. But when I run this command g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
it ask me groups... and that i thought is for fitting/// for example - ------------------------ Select group for least squares fit Group 0 (C-alpha_chain1) has 249 elements Group 1 (C-alpha_chain2) has 249 elements Group 2 (C-alpha_chain3) has 249 elements Group 3 (C-alpha_chain4) has 249 elements Select a group: 0 Selected 0: 'C-alpha_chain1' Select group for RMSD calculation Group 0 (C-alpha_chain1) has 249 elements Group 1 (C-alpha_chain2) has 249 elements Group 2 (C-alpha_chain3) has 249 elements Group 3 (C-alpha_chain4) has 249 elements Select a group:1 Selected 1: 'C-alpha_chain2' --------------------------------- Is it not superimposing these two chins and calculating RMSD between them??? -- anupam > On 9/05/2010 9:29 PM, Justin A. Lemkul wrote: >> >> >> Anupam Nath Jha wrote: >>>> >>>> Anupam Nath Jha wrote: >>>>> Dear all >>>>> >>>>> I made an index file with 4 different groups for 4 different chains >>>>> (since my >>>>> protein is a tetramer) and then run >>>>> >>>>> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out >>>>> >>>>> to get the rmsd between two different monomers from the same structure, >>>>> it asked me two different groups and I gave 0 and 1. >>>>> >>>>> The output file is like this >>>>> >>>>> # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New >>>>> # >>>>> # g_rms is part of G R O M A C S: >>>>> # >>>>> # Grunge ROck MAChoS >>>>> # >>>>> @ title "RMSD" >>>>> @ xaxis label "Time (ps)" >>>>> @ yaxis label "RMSD (nm)" >>>>> @TYPE xy >>>>> @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1" >>>>> 0.0000000 0.0000001 >>>>> >>>> In the command you've given (with the same file for -s and -f), >>>> you're computing >>>> the RMSD at time zero, after fitting to the structure at time zero, >>>> so the RMSD >>>> must be zero. >>> >>> >>> but I am giving different groups (as chains). I am trying to get RMSD >>> between >>> two monomers in same structure so what's wrong in that.... >>> >> >> It doesn't matter. The structure for calculation (-f) and the reference >> structure (-s) are identical, so the RMSD has to be zero, regardless of >> the fitting group and calculation groups chosen. > > Exactly. Only if you can fit group A from one file to group B from a > file (which may or may not be the same file) can Anupam do this > calculation. g_rms seems not to allow this. > > Instead, Anupam should use trjconv or editconf to select groups > beforehand, as I think I suggested a few days back. Thus (say) editconf > produces file_with_group_A.pdb and editconf produces > file_with_group_B.pdb, which allows g_rms -f file_with_group_A -s > file_with_group_B. This will work if the two groups have the same atoms > in matching orders, which should be the case for a tetramer setup. > > Mark > >>>>> so the rmsd = 0.0000001 >>>>> >>>>> whereas when I use online server it gives me 1.4. >>>>> >>>>> so what am I doing wrong? >>>>> >>>> Then whatever you're giving the online server is different. The Gromacs >>>> calculation seems to be correct. >>>> >>>> -Justin >>>> >>> >>> >>> >>>>> regrads >>>>> anupam >>>>> >>>>> >>>>> >>>> -- >>>> ======================================== >>>> >>>> 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/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 >>>> >>>> -- >>>> This message has been scanned for viruses and >>>> dangerous content by MailScanner, and is >>>> believed to be clean. >>>> >>>> >>> >>> >> > -- > 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 > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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
