you said you have used online server for superimposition ... which one you used... try TOPMATCH server....
On Sun, May 9, 2010 at 5:31 PM, Anupam Nath Jha <anu...@mbu.iisc.ernet.in>wrote: > > 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 > -- Bharath.K.Chakravarthi Ph:9535629260
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