[gmx-users] RMSF analysis
Hi all, I recently performed MD simulation of protein - ligand complex..and analyzed its trajectory using RMSF tool in gromacs. This analysis revealed particular residue in binding site of protein showed quite high fluctuation around 0.30 nm but other residues were in range of 0.15 to 0.20 Can any body explain why this particular residue have high RMSF value in compared to other residues Thanks, Nitin -- 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] RMSF analysis
On 10/9/13 3:29 PM, Sainitin Donakonda wrote: Hi all, I recently performed MD simulation of protein - ligand complex..and analyzed its trajectory using RMSF tool in gromacs. This analysis revealed particular residue in binding site of protein showed quite high fluctuation around 0.30 nm but other residues were in range of 0.15 to 0.20 Can any body explain why this particular residue have high RMSF value in compared to other residues Doubtful, at least not without considerably more information. What functional significance does it have, if any? What is the residue? What did you measure - RMSF of the whole residue, just the backbone, just C-alpha, etc? Higher RMSF means the residue flops around more, i.e. your outcome indicates that the residue deviates from the average position to a greater extent than the other residues. Whether or not this actually means anything at all depends on your knowledge of the nature of the protein-ligand complex and the answers to the questions posed above. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] RMSF analysis
What functional significance does it have, if any? --- According to my knowledge this reside is present in binding site.. and forms some hydrogen bonds with ligand What is the residue? -- *Glutamic Acid* What did you measure - RMSF of the whole residue, just the backbone, just C-alpha, etc? --* I measured Just C-alpha atoms.* Let me know On Wed, Oct 9, 2013 at 9:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/9/13 3:29 PM, Sainitin Donakonda wrote: Hi all, I recently performed MD simulation of protein - ligand complex..and analyzed its trajectory using RMSF tool in gromacs. This analysis revealed particular residue in binding site of protein showed quite high fluctuation around 0.30 nm but other residues were in range of 0.15 to 0.20 Can any body explain why this particular residue have high RMSF value in compared to other residues Doubtful, at least not without considerably more information. What functional significance does it have, if any? What is the residue? What did you measure - RMSF of the whole residue, just the backbone, just C-alpha, etc? Higher RMSF means the residue flops around more, i.e. your outcome indicates that the residue deviates from the average position to a greater extent than the other residues. Whether or not this actually means anything at all depends on your knowledge of the nature of the protein-ligand complex and the answers to the questions posed above. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] RMSF analysis
Is that residue in a loop? Gianluca On Wed, 9 Oct 2013, Sainitin Donakonda wrote: Hi all, I recently performed MD simulation of protein - ligand complex..and analyzed its trajectory using RMSF tool in gromacs. This analysis revealed particular residue in binding site of protein showed quite high fluctuation around 0.30 nm but other residues were in range of 0.15 to 0.20 Can any body explain why this particular residue have high RMSF value in compared to other residues Thanks, Nitin -- 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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- 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] RMSF analysis
On 10/9/13 4:09 PM, Sainitin Donakonda wrote: What functional significance does it have, if any? --- According to my knowledge this reside is present in binding site.. and forms some hydrogen bonds with ligand Do you observe hydrogen bonds with the ligand? What is the residue? -- *Glutamic Acid* What did you measure - RMSF of the whole residue, just the backbone, just C-alpha, etc? --* I measured Just C-alpha atoms.* So the backbone is fairly flexible. Glutamic acid residues are very flexible, though the flexibility is usually due to side chain motions, hence why they are among the more difficult residues to assign in crystal structures. Depending on the extent to which this residue is solvent exposed, this may explain your observations. But again, this is a complete guess and other factors may be significant here, including sampling time, whether or not you are eliminating some time at the start of the simulation to allow for unrestrained equilibration (VERY significant for quantities like RMSF), and whether or not the observation is reproducible in multiple simulations. The RMSF value you report is not especially large and may not mean anything at all, and its absolute value may not be convincing of any sort of argument. Whether or not it changes depending on conditions like presence or absence of a ligand may be more interesting, but as hopefully these last few sentences show, there is very little point in anyone guessing at functional implications from one vaguely described outcome ;) -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] rmsf analysis
to analyse the flexibility of the protein i used tge command g_rmsf -s md.tpr -f traj.xtc -oq but its showing that - can not open md.tpr file as i am new to it cant figure it outany suggestions... - thanks in advance :) -- View this message in context: http://gromacs.5086.n6.nabble.com/rmsf-analysis-tp5006285.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] rmsf analysis
Hi, It should be able to find md.tpr unless your file is named something else or you are issuing the command from other directory. On Wed, Mar 13, 2013 at 9:31 AM, vansh vsha...@imtech.res.in wrote: to analyse the flexibility of the protein i used tge command g_rmsf -s md.tpr -f traj.xtc -oq but its showing that - can not open md.tpr file as i am new to it cant figure it outany suggestions... - thanks in advance :) -- View this message in context: http://gromacs.5086.n6.nabble.com/rmsf-analysis-tp5006285.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 -- Ankita Naithani -- 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] RMSF: protein flexibility
as i want to analyse the local protein mobility, i used g_rmsf -s md.tpr -f traj.xtc -oq but its showing can not open file md.tpr...can anyone please suggest me from where to get md.tpr file ???/ -- View this message in context: http://gromacs.5086.n6.nabble.com/RMSF-protein-flexibility-tp5005815.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] RMSF error when fitting to average structure
Dear all, I have a 70 ns trajectory for which the last 60 ns appears to be equilibrated. I'm attempting to create a plot of RMSF but I want to align it to the equilibrated structure, not the starting structure. I first ran g_rmsf using the starting structure as the reference structure over only the last 60 ns and output the average structure (with B-factor column) using the -ox flag. I would now like to use this average, equilibrium structure as the reference structure for fitting the entire trajectory. When I try and use this average structure as a reference structure with the -s flag, I get the following error: WARNING: if there are broken molecules in the trajectory file, they can not be made whole without a run input file I'm not sure if the broken molecule it's referring to is the average structure, which I presume could be broken due to the unnatural bond lengths and angles resulting from averaging or if there's a problem trying to use a pdb file (which is the only -ox output file option) instead of a .tpr file, which is the format of the original starting structure, which worked. Does anyone have a suggestion as to how to obtain this rmsf plot? Thank you, Tom -- View this message in context: http://gromacs.5086.n6.nabble.com/RMSF-error-when-fitting-to-average-structure-tp5000251.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] RMSF error when fitting to average structure
On 8/16/12 10:13 AM, tdgrant1 wrote: Dear all, I have a 70 ns trajectory for which the last 60 ns appears to be equilibrated. I'm attempting to create a plot of RMSF but I want to align it to the equilibrated structure, not the starting structure. I first ran g_rmsf using the starting structure as the reference structure over only the last 60 ns and output the average structure (with B-factor column) using the -ox flag. I would now like to use this average, equilibrium structure as the reference structure for fitting the entire trajectory. When I try and use this average structure as a reference structure with the -s flag, I get the following error: WARNING: if there are broken molecules in the trajectory file, they can not be made whole without a run input file I'm not sure if the broken molecule it's referring to is the average structure, which I presume could be broken due to the unnatural bond lengths and angles resulting from averaging or if there's a problem trying to use a pdb file (which is the only -ox output file option) instead of a .tpr file, which is the format of the original starting structure, which worked. Does anyone have a suggestion as to how to obtain this rmsf plot? The warning about broken molecules relates to the trajectory (as stated in the message), so periodicity effects are not accounted for if you are not using a .tpr file. Thus you could get erroneous results unless you have already corrected for PBC effects using trjconv before running g_rmsf. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] RMSF calculations
Dear all, I have a set of proteins(in pdb format) in which some are solved by X-ray diffraction and some by NMR. I have done the md simulation of these proteins using gromacs for 30ns [For NMR structures, i have taken the first model as the starting structure] Now, that i want to calculate the RMSF value from the simulations and compare with the RMSF values from experimental structures [X-ray/NMR] For the proteins with crystal structures , calculation is done using using g_rmsf function and the comparison is done. and for protein from NMR structure , the RMSF values are calculated from the simulation trajectory. But in order to compare these, how does one get the RMSF values ? ,since the pdb file doesn't have the b-factors .. Is it a good idea to use the NMR ensembles ( usually 20 models from NMR) to derive the RMSF and compare these with simulation results ..? or is there any other parameter that i can calculate from NMR models, which is similar to RMSF ..? Thanksin advance .. Thanking You Gurunath -- 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] RMSF calculations
Hi Gurunath, Each structure in the NMR ensemble is a fit to the experimental data. Unlike an MD trajectory, you can not assume that the set of structures is a proper sample from the Boltzmann distribution, and therefore, the RMSF can not be expected to correspond to the RMSF of the system. Now, on a more qualitative level, it is likely that the parts that are less defined in the NMR ensemble will also have larger RMSFs than the rest, and could do for a rough comparison. Hope it helps, Tsjerk On Mon, Oct 10, 2011 at 12:22 PM, Gurunath Katagi gurukat...@gmail.com wrote: Dear all, I have a set of proteins(in pdb format) in which some are solved by X-ray diffraction and some by NMR. I have done the md simulation of these proteins using gromacs for 30ns [For NMR structures, i have taken the first model as the starting structure] Now, that i want to calculate the RMSF value from the simulations and compare with the RMSF values from experimental structures [X-ray/NMR] For the proteins with crystal structures , calculation is done using using g_rmsf function and the comparison is done. and for protein from NMR structure , the RMSF values are calculated from the simulation trajectory. But in order to compare these, how does one get the RMSF values ? ,since the pdb file doesn't have the b-factors .. Is it a good idea to use the NMR ensembles ( usually 20 models from NMR) to derive the RMSF and compare these with simulation results ..? or is there any other parameter that i can calculate from NMR models, which is similar to RMSF ..? Thanksin advance .. Thanking You Gurunath -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen 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
[gmx-users] RMSF: Different results for same residue
Hi, I am simulating a tetrameric protein in membrane. The simulation is for 30ns. I wish to calculate RMSF for just one monomer (A). I thought of doing this in two ways, 1. I input the residue numbers for the monomer A by creating an index.ndx file to calculate RMSF only for the selected monomer CA atoms. g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg -n index.ndx 2. I calculate RMSF for the complete protein CA atoms g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg I find the output from these to commands for the same monomer A residues are different. The second command calculates a very high RMSF for the same residues. Why is it so ?? Or am I making a mistake at some place ?? Thanks in advance. Alok -- 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] RMSF: Different results for same residue
Alok Jain wrote: Hi, I am simulating a tetrameric protein in membrane. The simulation is for 30ns. I wish to calculate RMSF for just one monomer (A). I thought of doing this in two ways, 1. I input the residue numbers for the monomer A by creating an index.ndx file to calculate RMSF only for the selected monomer CA atoms. g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg -n index.ndx 2. I calculate RMSF for the complete protein CA atoms g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg I find the output from these to commands for the same monomer A residues are different. The second command calculates a very high RMSF for the same residues. Why is it so ?? Or am I making a mistake at some place ?? The selected index group has a least-squares fit performed on it. If the fitting group is different, the output RMSF will be different. In case (1) you're doing the fitting and establishing a reference for RMSF from just one monomer and then doing the calculation on that group. In case (2) you're using the whole protein for the calculation. -Justin Thanks in advance. Alok -- 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
Re: [gmx-users] RMSF: Different results for same residue
Il 15/04/2011 18:45, Alok Jain ha scritto: Hi, I am simulating a tetrameric protein in membrane. The simulation is for 30ns. I wish to calculate RMSF for just one monomer (A). I thought of doing this in two ways, 1. I input the residue numbers for the monomer A by creating an index.ndx file to calculate RMSF only for the selected monomer CA atoms. g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg -n index.ndx 2. I calculate RMSF for the complete protein CA atoms g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg I find the output from these to commands for the same monomer A residues are different. The second command calculates a very high RMSF for the same residues. Why is it so ?? Or am I making a mistake at some place ?? Thanks in advance. Alok The reason is that in the two cases you used two different groups to fit the protein. Different fit generates different result. If you try to calculate RMSF, fitting on the subunit B, you will find a third result. I guess the subunit B should fluctuate less than case 2) -- 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] RMSF or RMSD per residues
Dear all I want to analyze the mobility of residues in various conditions. I need to know examining the RMSF is more useful or RMSD per residue? Thanks in advance Shiva -- 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] rmsf question
Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. Compared to this the RMSF of C-alpha computed from a MD trajectory reflects the geometric fluctuations of the backbone in the Boltzmann distribution of states in the generated ensemble. The uncertanty in the NMR structure can be influenced by the thermal fluctuations in the backbone geometry. Only in this respect the comparison of the two makes sense. Is this correct? Many thanks again for your comments! Andrei On Mon, Mar 15, 2010 at 10:00 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 15/03/2010 6:45 PM, Andrei Neamtu wrote: Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. Sure. I didn't imply you needed or wanted to. g_rmsf -f your.pdb -s some_suitable.file -n some.ndx g_rmsf -f your.xtc -s some_other_suitable.file -n some_other.ndx In certain cases you'll get to use the same -s or -n, or have to juggle atom orders. So, in the PDB file each 'frame' (MODEL) in the NMR file has the same order and number of atoms. This is also true for the MD trajectory. In the end i compare the two plots to see if the residues along the chain have comparable 'flexibility' Is necessary in this case to have a correspondence between the order of atoms in PDb and in MD trajectory? In this sense the comparison makes sense? (I mean if I do the residue mediation) You just need to make sure you are comparing equivalent things. If you just want (say) a C-alpha RMSF plot, then you can go ahead and do that if the index groups work. If you want all-atom RMSF then you might have some more fiddly work to do. Mark (The PDB is a NMR structure and so it has the hydorgen added and no missing side chains. And, it has the same number of atoms as the gro file generated with pdb2gmx. And also the same number of atoms in the corresponding residues.) Many thanks, Andrei On Sun, Mar 14, 2010 at 3:16 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison. If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter. Mark -- gmx-users mailing list gmx-us...@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 -- gmx-users mailing list gmx-us...@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 -- gmx-users mailing listgmx-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
Re: [gmx-users] rmsf question
On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote: Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. Well, the uncertainty of the NMR experiment would be strongly correlated with the dynamics of the system in solution, which in a sense reflects its fluctuations. This is different from an actual uncertainty of the experiment. Compared to this the RMSF of C-alpha computed from a MD trajectory reflects the geometric fluctuations of the backbone in the Boltzmann distribution of states in the generated ensemble. The uncertanty in the NMR structure can be influenced by the thermal fluctuations in the backbone geometry. Only in this respect the comparison of the two makes sense. Is this correct? Many thanks again for your comments! Andrei On Mon, Mar 15, 2010 at 10:00 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 15/03/2010 6:45 PM, Andrei Neamtu wrote: Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. Sure. I didn't imply you needed or wanted to. g_rmsf -f your.pdb -s some_suitable.file -n some.ndx g_rmsf -f your.xtc -s some_other_suitable.file -n some_other.ndx In certain cases you'll get to use the same -s or -n, or have to juggle atom orders. So, in the PDB file each 'frame' (MODEL) in the NMR file has the same order and number of atoms. This is also true for the MD trajectory. In the end i compare the two plots to see if the residues along the chain have comparable 'flexibility' Is necessary in this case to have a correspondence between the order of atoms in PDb and in MD trajectory? In this sense the comparison makes sense? (I mean if I do the residue mediation) You just need to make sure you are comparing equivalent things. If you just want (say) a C-alpha RMSF plot, then you can go ahead and do that if the index groups work. If you want all-atom RMSF then you might have some more fiddly work to do. Mark (The PDB is a NMR structure and so it has the hydorgen added and no missing side chains. And, it has the same number of atoms as the gro file generated with pdb2gmx. And also the same number of atoms in the corresponding residues.) Many thanks, Andrei On Sun, Mar 14, 2010 at 3:16 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison. If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter. 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/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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] rmsf question
On 16/03/2010 8:17 PM, XAvier Periole wrote: On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote: Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. Well, the uncertainty of the NMR experiment would be strongly correlated with the dynamics of the system in solution, which in a sense reflects its fluctuations. ... *if* there's reason to believe that the NMR ensemble reflects the Boltzmann ensemble. I've no idea how such software works, but I could certainly imagine algorithms that produced a set of plausible structures by varying things that have little or nothing to do with physics... starting points for constrained geometry optimizations, for example. Mark This is different from an actual uncertainty of the experiment. Compared to this the RMSF of C-alpha computed from a MD trajectory reflects the geometric fluctuations of the backbone in the Boltzmann distribution of states in the generated ensemble. The uncertanty in the NMR structure can be influenced by the thermal fluctuations in the backbone geometry. Only in this respect the comparison of the two makes sense. Is this correct? Many thanks again for your comments! Andrei On Mon, Mar 15, 2010 at 10:00 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 15/03/2010 6:45 PM, Andrei Neamtu wrote: Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. Sure. I didn't imply you needed or wanted to. g_rmsf -f your.pdb -s some_suitable.file -n some.ndx g_rmsf -f your.xtc -s some_other_suitable.file -n some_other.ndx In certain cases you'll get to use the same -s or -n, or have to juggle atom orders. So, in the PDB file each 'frame' (MODEL) in the NMR file has the same order and number of atoms. This is also true for the MD trajectory. In the end i compare the two plots to see if the residues along the chain have comparable 'flexibility' Is necessary in this case to have a correspondence between the order of atoms in PDb and in MD trajectory? In this sense the comparison makes sense? (I mean if I do the residue mediation) You just need to make sure you are comparing equivalent things. If you just want (say) a C-alpha RMSF plot, then you can go ahead and do that if the index groups work. If you want all-atom RMSF then you might have some more fiddly work to do. Mark (The PDB is a NMR structure and so it has the hydorgen added and no missing side chains. And, it has the same number of atoms as the gro file generated with pdb2gmx. And also the same number of atoms in the corresponding residues.) Many thanks, Andrei On Sun, Mar 14, 2010 at 3:16 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison. If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter. Mark -- 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 -- 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 -- 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 -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] rmsf question
On Mar 16, 2010, at 10:24 AM, Mark Abraham wrote: On 16/03/2010 8:17 PM, XAvier Periole wrote: On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote: Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. Well, the uncertainty of the NMR experiment would be strongly correlated with the dynamics of the system in solution, which in a sense reflects its fluctuations. ... *if* there's reason to believe that the NMR ensemble reflects the Boltzmann ensemble. just as much as MD simulations. I've no idea how such software works, but I could certainly imagine algorithms that produced a set of plausible structures by varying things that have little or nothing to do with physics... starting points for constrained geometry optimizations, for example. Mark This is different from an actual uncertainty of the experiment. Compared to this the RMSF of C-alpha computed from a MD trajectory reflects the geometric fluctuations of the backbone in the Boltzmann distribution of states in the generated ensemble. The uncertanty in the NMR structure can be influenced by the thermal fluctuations in the backbone geometry. Only in this respect the comparison of the two makes sense. Is this correct? Many thanks again for your comments! Andrei On Mon, Mar 15, 2010 at 10:00 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 15/03/2010 6:45 PM, Andrei Neamtu wrote: Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. Sure. I didn't imply you needed or wanted to. g_rmsf -f your.pdb -s some_suitable.file -n some.ndx g_rmsf -f your.xtc -s some_other_suitable.file -n some_other.ndx In certain cases you'll get to use the same -s or -n, or have to juggle atom orders. So, in the PDB file each 'frame' (MODEL) in the NMR file has the same order and number of atoms. This is also true for the MD trajectory. In the end i compare the two plots to see if the residues along the chain have comparable 'flexibility' Is necessary in this case to have a correspondence between the order of atoms in PDb and in MD trajectory? In this sense the comparison makes sense? (I mean if I do the residue mediation) You just need to make sure you are comparing equivalent things. If you just want (say) a C-alpha RMSF plot, then you can go ahead and do that if the index groups work. If you want all-atom RMSF then you might have some more fiddly work to do. Mark (The PDB is a NMR structure and so it has the hydorgen added and no missing side chains. And, it has the same number of atoms as the gro file generated with pdb2gmx. And also the same number of atoms in the corresponding residues.) Many thanks, Andrei On Sun, Mar 14, 2010 at 3:16 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison. If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter. Mark -- 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 -- 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 -- 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
Re: [gmx-users] rmsf question
Hi Andrei, If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. No, that's not what I said. You're saying that there's one structure (the structure), but there is uncertainty in resolving it. That's not the case. There is a distribution of structures that gives rise to a set of signals, from which time and ensemble averaged distances between certain pairs of atoms can be deduced. But this set of distances is typically leaves a number of degrees of freedom, and on top of that the time averaging may actually yield restraints that cannot be satisfied simultaneously. So, structures have to be fit to the set of distances, which is typically repeated a large number of times using simulated annealing with different starting conditions. From the resulting set the ones best fitting the data are selected and put forward as a representative set of structures. The least defined regions, in terms of (distance) restraints are likely to show most variation. But the structures are not weighted according to their probabilities and therefore neither the average nor the fluctuations can be expected to coincide with the moments of the Boltzmann distribution. Compared to this the RMSF of C-alpha computed from a MD trajectory reflects the geometric fluctuations of the backbone in the Boltzmann distribution of states in the generated ensemble. Assuming you have sampled long enough and not just trying to explain drift as fluctuation :) The uncertanty in the NMR structure can be influenced by the thermal fluctuations in the backbone geometry. Well, that's part of it, but the way the models are derived contributes a lot. Only in this respect the comparison of the two makes sense. Is this correct? Comparisons can be made, but you have to formulate and justify your assumptions. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-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
Re: [gmx-users] rmsf question
Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. So, in the PDB file each 'frame' (MODEL) in the NMR file has the same order and number of atoms. This is also true for the MD trajectory. In the end i compare the two plots to see if the residues along the chain have comparable 'flexibility' Is necessary in this case to have a correspondence between the order of atoms in PDb and in MD trajectory? In this sense the comparison makes sense? (I mean if I do the residue mediation) (The PDB is a NMR structure and so it has the hydorgen added and no missing side chains. And, it has the same number of atoms as the gro file generated with pdb2gmx. And also the same number of atoms in the corresponding residues.) Many thanks, Andrei On Sun, Mar 14, 2010 at 3:16 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison. If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter. Mark -- gmx-users mailing list gmx-us...@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 -- gmx-users mailing listgmx-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
Re: [gmx-users] rmsf question
Hi Andrei, You can do it this way. But do mind that the ensemble from NMR is not meant to reflect the Boltzmann distribution. Rather it is meant to provide a number of plausible solutions given the (positive) restraints from the experiments and the force field used for the refinement. This means that the moments of the distribution (mean and fluctuation) need not be comparable quantitatively. A more direct comparison between experiments and simulations could be obtained by comparing backbone order parameters. Cheers, Tsjerk On Mon, Mar 15, 2010 at 8:45 AM, Andrei Neamtu neamtuand...@gmail.com wrote: Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. So, in the PDB file each 'frame' (MODEL) in the NMR file has the same order and number of atoms. This is also true for the MD trajectory. In the end i compare the two plots to see if the residues along the chain have comparable 'flexibility' Is necessary in this case to have a correspondence between the order of atoms in PDb and in MD trajectory? In this sense the comparison makes sense? (I mean if I do the residue mediation) (The PDB is a NMR structure and so it has the hydorgen added and no missing side chains. And, it has the same number of atoms as the gro file generated with pdb2gmx. And also the same number of atoms in the corresponding residues.) Many thanks, Andrei On Sun, Mar 14, 2010 at 3:16 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison. If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter. Mark -- gmx-users mailing list gmx-us...@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 -- gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-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
Re: [gmx-users] rmsf question
On 15/03/2010 6:45 PM, Andrei Neamtu wrote: Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. Sure. I didn't imply you needed or wanted to. g_rmsf -f your.pdb -s some_suitable.file -n some.ndx g_rmsf -f your.xtc -s some_other_suitable.file -n some_other.ndx In certain cases you'll get to use the same -s or -n, or have to juggle atom orders. So, in the PDB file each 'frame' (MODEL) in the NMR file has the same order and number of atoms. This is also true for the MD trajectory. In the end i compare the two plots to see if the residues along the chain have comparable 'flexibility' Is necessary in this case to have a correspondence between the order of atoms in PDb and in MD trajectory? In this sense the comparison makes sense? (I mean if I do the residue mediation) You just need to make sure you are comparing equivalent things. If you just want (say) a C-alpha RMSF plot, then you can go ahead and do that if the index groups work. If you want all-atom RMSF then you might have some more fiddly work to do. Mark (The PDB is a NMR structure and so it has the hydorgen added and no missing side chains. And, it has the same number of atoms as the gro file generated with pdb2gmx. And also the same number of atoms in the corresponding residues.) Many thanks, Andrei On Sun, Mar 14, 2010 at 3:16 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison. If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter. 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/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 -- gmx-users mailing listgmx-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
[gmx-users] rmsf question
Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? g_rmsf needs a .tpr file. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. Thanks, Andrei -- gmx-users mailing listgmx-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
Re: [gmx-users] rmsf question
On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison. If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter. 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/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
Re: Re: [gmx-users] RMSF reference state?
Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this?With the option -od the root mean square deviation with respect to the reference structure is calculated What about without -od, should there be no reference structure or the reference structure is taken as average over the trajectory? Thanks! Pan Wu wrote: Hi everyone, Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame. So in this way, can I choose the reference frame from *.tpr file or the coordinate average over the whole trajectory? If Gromacs can, how? I believe the reference structure is taken from whatever structure file is given to the -s flag, so in principle you could provide any frame from the trajectory, as well as the initial one, or some average structure (from, i.e. g_cluster or something similar). -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/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
Re: Re: [gmx-users] RMSF reference state?
Hi Pan Wu, There are two things to distinguish: 1. The reference structure used to remove translational and rotational degrees of freedom 2. The reference against which the deviations (on a per atom base) are calculated that are then squared, averaged and taken the root of (root mean square fluctuation). These two need not be the same. It is common, and most sensible, to calculate the deviations against the average structure, after fitting all structures in the trajectory against a certain reference structure. With option -od the deviations against the reference used for fitting are calculated rather than against the average. You do need a reference for fitting, since otherwise you include overall rotation and translation in the calculation of the RMSF, which you usually wouldn't want. I hope this makes it clear. Cheers, Tsjerk On Wed, Oct 14, 2009 at 9:12 PM, Pan Wu pan...@duke.edu wrote: Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this? With the option -od the root mean square deviation with respect to the reference structure is calculated What about without -od, should there be no reference structure or the reference structure is taken as average over the trajectory? Thanks! Pan Wu wrote: Hi everyone, Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame. So in this way, can I choose the reference frame from *.tpr file or the coordinate average over the whole trajectory? If Gromacs can, how? I believe the reference structure is taken from whatever structure file is given to the -s flag, so in principle you could provide any frame from the trajectory, as well as the initial one, or some average structure (from, i.e. g_cluster or something similar). -Justin ___ gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-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
Re: [gmx-users] RMSF reference state?
Pan Wu wrote: Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this? With the option -od the root mean square deviation with respect to the reference structure is calculated What about without -od, should there be no reference structure or the reference structure is taken as average over the trajectory? You're talking about two separate calculations. Using -od calculates some sort of RMSD. If you do not use -od, then the standard output (-o) is RMSF, using the fitting described (unless you use -nofit). -Justin Thanks! Pan Wu wrote: Hi everyone, Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame. So in this way, can I choose the reference frame from *.tpr file or the coordinate average over the whole trajectory? If Gromacs can, how? I believe the reference structure is taken from whatever structure file is given to the -s flag, so in principle you could provide any frame from the trajectory, as well as the initial one, or some average structure (from, i.e. g_cluster or something similar). -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/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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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
Re: [gmx-users] RMSF reference state?
Hi, Actually, Justin is completely right (and I should've checked g_rmsf -h). -od calculates the RMSD from the structure in the frame against the structure in the topology file. This does not nullify the statements regarding references for fitting and references for deviations though :p Cheers, Tsjerk On Wed, Oct 14, 2009 at 9:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Pan Wu wrote: Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this? With the option -od the root mean square deviation with respect to the reference structure is calculated What about without -od, should there be no reference structure or the reference structure is taken as average over the trajectory? You're talking about two separate calculations. Using -od calculates some sort of RMSD. If you do not use -od, then the standard output (-o) is RMSF, using the fitting described (unless you use -nofit). -Justin Thanks! Pan Wu wrote: Hi everyone, Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame. So in this way, can I choose the reference frame from *.tpr file or the coordinate average over the whole trajectory? If Gromacs can, how? I believe the reference structure is taken from whatever structure file is given to the -s flag, so in principle you could provide any frame from the trajectory, as well as the initial one, or some average structure (from, i.e. g_cluster or something similar). -Justin ___ gmx-users mailing list gmx-us...@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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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-us...@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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-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
[gmx-users] RMSF reference state?
Hi everyone,Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame. So in this way, can I choose the reference frame from *.tpr file or the coordinate average over the whole trajectory? If Gromacs can, how? Thank you in advance! -- Sincerely = Pan Wu Graduate Student in Department of Chemistry Duke University 124 Science Drive 5301 French Family Science Center Durham, NC 27708 Phone: (919) 660-1583 = ___ gmx-users mailing listgmx-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
Re: [gmx-users] RMSF reference state?
Pan Wu wrote: Hi everyone, Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame. So in this way, can I choose the reference frame from *.tpr file or the coordinate average over the whole trajectory? If Gromacs can, how? I believe the reference structure is taken from whatever structure file is given to the -s flag, so in principle you could provide any frame from the trajectory, as well as the initial one, or some average structure (from, i.e. g_cluster or something similar). -Justin Thank you in advance! -- Sincerely = Pan Wu Graduate Student in Department of Chemistry Duke University 124 Science Drive 5301 French Family Science Center Durham, NC 27708 Phone: (919) 660-1583 = ___ gmx-users mailing listgmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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
[gmx-users] rmsf
Hello I want to analyze the RMSF fluctuation of each residue of a protein during a simulation run. I am giving the command g_rmsf -f md.xtc -s md.tpr -b 4000 -e 6000 -o traj_rmsf.xvg -ox traj_avg.pdb. Then I am selecting the whole protein for the analysis. I am getting the RMSF per atom in the .xvg file and I have to plot the graph as RMSF versus atom no. but I want to have the RMSF of each amino acid residue.How Can I get the RMSF of each residue , what is the command for that? Subarna Connect more, do more and share more with Yahoo! India Mail. Learn more. http://in.overview.mail.yahoo.com/___ gmx-users mailing listgmx-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
[gmx-users] RMSF and temperature factors
Dear users, I have been trying to find information about the equation, which is used in GROMACS to converts RMSF values to temperature factors. I know NAMD uses: B = (RMSF2 x 8π2)/3 and would like to know if the same is used in GROMACS. Cheers, Una begin:vcard fn:Una Bjarnadottir n:Bjarnadottir;Una org:School of Biomolecular and Biomedical Science;Conway Institute adr:Belfield;;UCD ;Dublin;;4;Ireland email;internet:una.bjarnadot...@ucd.ie tel;work:+353 1 716 6874 tel;fax:+353 1 716 6898 version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] RMSF and temperature factors
Una Bjarnadottir wrote: Dear users, I have been trying to find information about the equation, which is used in GROMACS to converts RMSF values to temperature factors. I know NAMD uses: B = (RMSF2 x 8π2)/3 and would like to know if the same is used in GROMACS. Of course. Cheers, Una ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
