Re: [gmx-users] g_sas : Total surface area
On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I was calculating solvent accessible surface area for a trajectory using g_sas. I used an index file with 3 sets (A, B, C) of mutually exclusive residues but summing up to 20 amino acids. Then using g_sas calculated sas for these 3 sets separately and whole protein separately for the same trajectory. I was expecting that the average value of Total surface area (protein) ~ Total surface area (A)+Total surface area (B)+Total surface area (C) But it is not so. Could anyone explain me why? Not without seeing any numbers. You're probably thinking that the surface area of A excludes the interfacial area to the other sets, but it doesn't. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_sas : Total surface area
Hi Kavya, Can you better describe your system? As Mark suggested, could you supply some number? Francesco 2012/12/12 Mark Abraham mark.j.abra...@gmail.com On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I was calculating solvent accessible surface area for a trajectory using g_sas. I used an index file with 3 sets (A, B, C) of mutually exclusive residues but summing up to 20 amino acids. Then using g_sas calculated sas for these 3 sets separately and whole protein separately for the same trajectory. I was expecting that the average value of Total surface area (protein) ~ Total surface area (A)+Total surface area (B)+Total surface area (C) But it is not so. Could anyone explain me why? Not without seeing any numbers. You're probably thinking that the surface area of A excludes the interfacial area to the other sets, but it doesn't. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- 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] g_sas : Total surface area
Thank you very much for your replies. The system consists of a homodimer in tip4p dodecahedron box simulated using OPLSAA ff. The A B C here are the amino acids: A- S T N Q G P H B- A V L I M C F Y W C- D E K R So these are set in an index file and i used each one of these to calculate sasa in g_sas. When the g_sas calculation starts it specifies the number of hydrophobic atoms, one of the example - For the whole protein - 4644 out of 7590 atoms were classified as hydrophobic For group A of same protein - 702 out of 1424 atoms were classified as hydrophobic For group B of same protein - 2614 out of 3496 atoms were classified as hydrophobic For group C of same protein - 1328 out of 2670 atoms were classified as hydrophobic In this the number of hydrophobic atoms of A, B and C adds up to the total hydrophobic atoms in whole protein. but after the calculation is over the average values of Total sas (legend S2 of area.xvg file) of the protein and Total sas of A, B and C are given below Whole protein - 254.04nm^(-2) A - 175.87nm^(-2) B - 211.33nm^(-2) C - 264.65nm^(-2) I expected that the average total sas of Whole protein atleast approximately equal the sum of Total sas of A, B and C. If not why? All calculations are done for the same trajectory after equilibrating. Thank you Kavya On Wed, Dec 12, 2012 at 5:20 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi Kavya, Can you better describe your system? As Mark suggested, could you supply some number? Francesco 2012/12/12 Mark Abraham mark.j.abra...@gmail.com On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I was calculating solvent accessible surface area for a trajectory using g_sas. I used an index file with 3 sets (A, B, C) of mutually exclusive residues but summing up to 20 amino acids. Then using g_sas calculated sas for these 3 sets separately and whole protein separately for the same trajectory. I was expecting that the average value of Total surface area (protein) ~ Total surface area (A)+Total surface area (B)+Total surface area (C) But it is not so. Could anyone explain me why? Not without seeing any numbers. You're probably thinking that the surface area of A excludes the interfacial area to the other sets, but it doesn't. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- 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 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] g_sas : Total surface area
On 12/12/12 9:37 AM, Kavyashree M wrote: Thank you very much for your replies. The system consists of a homodimer in tip4p dodecahedron box simulated using OPLSAA ff. The A B C here are the amino acids: A- S T N Q G P H B- A V L I M C F Y W C- D E K R So these are set in an index file and i used each one of these to calculate sasa in g_sas. When the g_sas calculation starts it specifies the number of hydrophobic atoms, one of the example - For the whole protein - 4644 out of 7590 atoms were classified as hydrophobic For group A of same protein - 702 out of 1424 atoms were classified as hydrophobic For group B of same protein - 2614 out of 3496 atoms were classified as hydrophobic For group C of same protein - 1328 out of 2670 atoms were classified as hydrophobic In this the number of hydrophobic atoms of A, B and C adds up to the total hydrophobic atoms in whole protein. but after the calculation is over the average values of Total sas (legend S2 of area.xvg file) of the protein and Total sas of A, B and C are given below Whole protein - 254.04nm^(-2) A - 175.87nm^(-2) B - 211.33nm^(-2) C - 264.65nm^(-2) I expected that the average total sas of Whole protein atleast approximately equal the sum of Total sas of A, B and C. If not why? All calculations are done for the same trajectory after equilibrating. Are you selecting the correct groups when running g_sas? For instance, you should be selecting Protein for the surface calculation, and then your custom subsets for output. If you use the subsets for both surface calculation and output, you will get an artificially inflated value that includes extra surface area that is actually buried in the context of the whole structure. -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 * 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] g_sas : Total surface area
Sir, Oh! I was using sunset index numbers for both. I am sorry. I will try that and see. First option as protein and next the subset. Thank you very much. Kavya On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/12/12 9:37 AM, Kavyashree M wrote: Thank you very much for your replies. The system consists of a homodimer in tip4p dodecahedron box simulated using OPLSAA ff. The A B C here are the amino acids: A- S T N Q G P H B- A V L I M C F Y W C- D E K R So these are set in an index file and i used each one of these to calculate sasa in g_sas. When the g_sas calculation starts it specifies the number of hydrophobic atoms, one of the example - For the whole protein - 4644 out of 7590 atoms were classified as hydrophobic For group A of same protein - 702 out of 1424 atoms were classified as hydrophobic For group B of same protein - 2614 out of 3496 atoms were classified as hydrophobic For group C of same protein - 1328 out of 2670 atoms were classified as hydrophobic In this the number of hydrophobic atoms of A, B and C adds up to the total hydrophobic atoms in whole protein. but after the calculation is over the average values of Total sas (legend S2 of area.xvg file) of the protein and Total sas of A, B and C are given below Whole protein - 254.04nm^(-2) A - 175.87nm^(-2) B - 211.33nm^(-2) C - 264.65nm^(-2) I expected that the average total sas of Whole protein atleast approximately equal the sum of Total sas of A, B and C. If not why? All calculations are done for the same trajectory after equilibrating. Are you selecting the correct groups when running g_sas? For instance, you should be selecting Protein for the surface calculation, and then your custom subsets for output. If you use the subsets for both surface calculation and output, you will get an artificially inflated value that includes extra surface area that is actually buried in the context of the whole structure. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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] g_sas : Total surface area
I meant subset :) On Wed, Dec 12, 2012 at 8:21 PM, Kavyashree M hmkv...@gmail.com wrote: Sir, Oh! I was using sunset index numbers for both. I am sorry. I will try that and see. First option as protein and next the subset. Thank you very much. Kavya On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/12/12 9:37 AM, Kavyashree M wrote: Thank you very much for your replies. The system consists of a homodimer in tip4p dodecahedron box simulated using OPLSAA ff. The A B C here are the amino acids: A- S T N Q G P H B- A V L I M C F Y W C- D E K R So these are set in an index file and i used each one of these to calculate sasa in g_sas. When the g_sas calculation starts it specifies the number of hydrophobic atoms, one of the example - For the whole protein - 4644 out of 7590 atoms were classified as hydrophobic For group A of same protein - 702 out of 1424 atoms were classified as hydrophobic For group B of same protein - 2614 out of 3496 atoms were classified as hydrophobic For group C of same protein - 1328 out of 2670 atoms were classified as hydrophobic In this the number of hydrophobic atoms of A, B and C adds up to the total hydrophobic atoms in whole protein. but after the calculation is over the average values of Total sas (legend S2 of area.xvg file) of the protein and Total sas of A, B and C are given below Whole protein - 254.04nm^(-2) A - 175.87nm^(-2) B - 211.33nm^(-2) C - 264.65nm^(-2) I expected that the average total sas of Whole protein atleast approximately equal the sum of Total sas of A, B and C. If not why? All calculations are done for the same trajectory after equilibrating. Are you selecting the correct groups when running g_sas? For instance, you should be selecting Protein for the surface calculation, and then your custom subsets for output. If you use the subsets for both surface calculation and output, you will get an artificially inflated value that includes extra surface area that is actually buried in the context of the whole structure. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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
