Re: [gmx-users] Solvent Accessible Area with different Claculation Groups
Quoting Benjamin Lindner b...@benlabs.net: Hi, let me add some information here to clarify the problem we're facing: I was wondering if anyone has some insight on why the two sasa values are not identical. From g_sas -h: The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. So, setting the calculation group to only include mol1 is simply incorrect usage of the program. Yes and no. We don't know whether the algorithm has any hidden assumptions, e.g. that all non-selected atoms are solvent molecules - that's why we are posting this maybe someone has intricate knowledge which might explain the odd result. @Justin, since you argued that the usage is incorrect: Can you answer why? As we understand it, the selection groups should identify the solvent atoms (by not selecting them) and identify which atoms should contribute to the total surface area (running sum). From the help information quoted above, the calculation group should be all non-solvent atoms. So if you're only selecting mol1 (which does not comprise the entirety of non-solvent atoms) then you're not specifying the right information. The program then assumes that everything else (that wasn't selected) is to be considered solvent. Thus, if you have mol1 and mol2 in pure water, then a group of mol1+mol2 must be the calculation group, and (per the documentation), either of those molecules can be the output group. -Justin I'm not sure this is correct actually (although there has been a bug in the program for a long time). But if you want to e.g. compute the occluded area in a protein-protein interaction you have to compute A+B-AB where A is the area of just protein A, ignoring everything else and so on. The fact the OP does not get the same area (did he use the same molecules?) is probably just poor sampling. Just wait a couple of hundred nanoseconds and see whether the distributions overlap. We didn't do any averaging. The results we get are by frame/timestep. In particular: case a) system group: A, output group: A case b) system group: AB, output group: A It is possible for case b) to produce higher numbers for SASA than case a) for the same frames. However, this defies our logic: How can an addition of steric atoms (molecule B) increase the total SASA of A? That's why we're puzzled. Cheers, Benjamin -Justin I am attaching a figure displaying the calculations described above, obtained by: g_sas -f /traj-0-37 -s top.tpr -n index-1-2.ndx -b 0 -e 100 -ndots 24 Many thanks for your help, Loukas Loukas Petridis Post-doctoral Research Fellow Center for Molecular Biophysics, Oak Ridge National Laboratory Building 6011, MS 6309, Oak Ridge, TN 37831 865-576-2576 http://cmb.ornl.gov/people/lpk -- 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.se sp...@gromacs.org http://folding.bmc.uu.se -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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 Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@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] Solvent Accessible Area with different Claculation Groups
Hi, let me add some information here to clarify the problem we're facing: I was wondering if anyone has some insight on why the two sasa values are not identical. From g_sas -h: The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. So, setting the calculation group to only include mol1 is simply incorrect usage of the program. Yes and no. We don't know whether the algorithm has any hidden assumptions, e.g. that all non-selected atoms are solvent molecules - that's why we are posting this maybe someone has intricate knowledge which might explain the odd result. @Justin, since you argued that the usage is incorrect: Can you answer why? As we understand it, the selection groups should identify the solvent atoms (by not selecting them) and identify which atoms should contribute to the total surface area (running sum). I'm not sure this is correct actually (although there has been a bug in the program for a long time). But if you want to e.g. compute the occluded area in a protein-protein interaction you have to compute A+B-AB where A is the area of just protein A, ignoring everything else and so on. The fact the OP does not get the same area (did he use the same molecules?) is probably just poor sampling. Just wait a couple of hundred nanoseconds and see whether the distributions overlap. We didn't do any averaging. The results we get are by frame/timestep. In particular: case a) system group: A, output group: A case b) system group: AB, output group: A It is possible for case b) to produce higher numbers for SASA than case a) for the same frames. However, this defies our logic: How can an addition of steric atoms (molecule B) increase the total SASA of A? That's why we're puzzled. Cheers, Benjamin -Justin I am attaching a figure displaying the calculations described above, obtained by: g_sas -f /traj-0-37 -s top.tpr -n index-1-2.ndx -b 0 -e 100 -ndots 24 Many thanks for your help, Loukas Loukas Petridis Post-doctoral Research Fellow Center for Molecular Biophysics, Oak Ridge National Laboratory Building 6011, MS 6309, Oak Ridge, TN 37831 865-576-2576 http://cmb.ornl.gov/people/lpk -- 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.se sp...@gromacs.org http://folding.bmc.uu.se -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Solvent Accessible Area with different Claculation Groups
Hi, We are examining a system comprising of two molecules (called mol1 and mol2) in water that are initially separated by 1.5nm. We calculate the surface accessible area of the first molecule ( mol1) in two ways: (a) sasa_a: by setting both the output and calculation groups to mol 1 (b) sasa_b: setting the calculation group to mol1 and mol2, and output group to mol1 During the simulation, the molecules are separated by more 1.5nm and since the probe radius = 0.14nm, we expected the values of the two surface areas to be identical. Instead we found sasa_a and sasa_b to differ by about +- 1.5 nm^2. Although this variation is small compared to the mean value ~86 nm^2, it has caused us some concern. We were also surprised that sasa_b was larger than sasa_a for part of the simulation. (The same trend is observed when the accuracy of the calculation was increased by using ndots=48). I was wondering if anyone has some insight on why the two sasa values are not identical. I am attaching a figure displaying the calculations described above, obtained by: g_sas -f /traj-0-37 -s top.tpr -n index-1-2.ndx -b 0 -e 100 -ndots 24 Many thanks for your help, Loukas Loukas Petridis Post-doctoral Research Fellow Center for Molecular Biophysics, Oak Ridge National Laboratory Building 6011, MS 6309, Oak Ridge, TN 37831 865-576-2576 http://cmb.ornl.gov/people/lpk attachment: sasa.pngattachment: mindist.png-- 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] Solvent Accessible Area with different Claculation Groups
Petridis, Loukas wrote: Hi, We are examining a system comprising of two molecules (called mol1 and mol2) in water that are initially separated by 1.5nm. We calculate the surface accessible area of the first molecule ( mol1) in two ways: (a) sasa_a: by setting both the output and calculation groups to mol 1 (b) sasa_b: setting the calculation group to mol1 and mol2, and output group to mol1 During the simulation, the molecules are separated by more 1.5nm and since the probe radius = 0.14nm, we expected the values of the two surface areas to be identical. Instead we found sasa_a and sasa_b to differ by about +- 1.5 nm^2. Although this variation is small compared to the mean value ~86 nm^2, it has caused us some concern. We were also surprised that sasa_b was larger than sasa_a for part of the simulation. (The same trend is observed when the accuracy of the calculation was increased by using ndots=48). I was wondering if anyone has some insight on why the two sasa values are not identical. From g_sas -h: The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. So, setting the calculation group to only include mol1 is simply incorrect usage of the program. -Justin I am attaching a figure displaying the calculations described above, obtained by: g_sas -f /traj-0-37 -s top.tpr -n index-1-2.ndx -b 0 -e 100 -ndots 24 Many thanks for your help, Loukas Loukas Petridis Post-doctoral Research Fellow Center for Molecular Biophysics, Oak Ridge National Laboratory Building 6011, MS 6309, Oak Ridge, TN 37831 865-576-2576 http://cmb.ornl.gov/people/lpk -- 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/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] Solvent Accessible Area with different Claculation Groups
Justin A. Lemkul wrote: Petridis, Loukas wrote: Hi, We are examining a system comprising of two molecules (called mol1 and mol2) in water that are initially separated by 1.5nm. We calculate the surface accessible area of the first molecule ( mol1) in two ways: (a) sasa_a: by setting both the output and calculation groups to mol 1 (b) sasa_b: setting the calculation group to mol1 and mol2, and output group to mol1 During the simulation, the molecules are separated by more 1.5nm and since the probe radius = 0.14nm, we expected the values of the two surface areas to be identical. Instead we found sasa_a and sasa_b to differ by about +- 1.5 nm^2. Although this variation is small compared to the mean value ~86 nm^2, it has caused us some concern. We were also surprised that sasa_b was larger than sasa_a for part of the simulation. (The same trend is observed when the accuracy of the calculation was increased by using ndots=48). I was wondering if anyone has some insight on why the two sasa values are not identical. From g_sas -h: The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. So, setting the calculation group to only include mol1 is simply incorrect usage of the program. I'm not sure this is correct actually (although there has been a bug in the program for a long time). But if you want to e.g. compute the occluded area in a protein-protein interaction you have to compute A+B-AB where A is the area of just protein A, ignoring everything else and so on. The fact the OP does not get the same area (did he use the same molecules?) is probably just poor sampling. Just wait a couple of hundred nanoseconds and see whether the distributions overlap. -Justin I am attaching a figure displaying the calculations described above, obtained by: g_sas -f /traj-0-37 -s top.tpr -n index-1-2.ndx -b 0 -e 100 -ndots 24 Many thanks for your help, Loukas Loukas Petridis Post-doctoral Research Fellow Center for Molecular Biophysics, Oak Ridge National Laboratory Building 6011, MS 6309, Oak Ridge, TN 37831 865-576-2576 http://cmb.ornl.gov/people/lpk -- 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://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
