[gmx-users] RE: Re: Binding Energy to Binding affinity (Kd) (Justin Lemkul)
Justin Lemkul wrote On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote: Hi Justin, I used ~20 windows to sample ~2 nm pulling. I notice that the distance between the complex being increased during the pulling but not gradually. At the distance of 0-1nm, there are 70 snapshots (the distance sometime increased sometimes decreased). At the distance of 1-2nm, there are only 30 snapshots (the distance kept increasing always). At the distance more than 3nm, the distance increased as 0.3nm of each snapshot, is it normal and reliable? I will assume you are using a harmonic potential (umbrella) to do the pulling. In this case, your observations are totally normal. When two species interact strongly, it is harder to pull them apart, thus the spring extends further to induce a larger force before displacement occurs. As the restoring forces are overcome, it is easier to move the pulled group through solution, so it makes more steady progress as the molecules are separated. Hi Justin, it is right I am using umbrella pulling. Now here is another hurdle in front of me: How to select the snapshots for umbrella samples? Since the distance between two groups went higher or lower at the beginning of the pulling. For example, during the pulling simulation, the distance changes like: 0.46 0.42 0.46 0.43 0.44 0.42 0.45 0.44 0.43 0.45 0.44 0.45 0.43 0.44 0.44 0.54 0.52 0.63 0.65 0.72 0.8 0.92 1.2 1.5 (nm) . I suppose it doesn't matter which snapshots to be chosen, as long as the snapshots can indicate a good spacing, the PMF result always should be same, right? Thanks, jiang. -- View this message in context: http://gromacs.5086.n6.nabble.com/RE-Re-Binding-Energy-to-Binding-affinity-Kd-Justin-Lemkul-tp5001504p5001632.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] RE: Re: Binding Energy to Binding affinity (Kd) (Justin Lemkul)
On 10/4/12 10:52 AM, jiang wrote: Justin Lemkul wrote On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote: Hi Justin, I used ~20 windows to sample ~2 nm pulling. I notice that the distance between the complex being increased during the pulling but not gradually. At the distance of 0-1nm, there are 70 snapshots (the distance sometime increased sometimes decreased). At the distance of 1-2nm, there are only 30 snapshots (the distance kept increasing always). At the distance more than 3nm, the distance increased as 0.3nm of each snapshot, is it normal and reliable? I will assume you are using a harmonic potential (umbrella) to do the pulling. In this case, your observations are totally normal. When two species interact strongly, it is harder to pull them apart, thus the spring extends further to induce a larger force before displacement occurs. As the restoring forces are overcome, it is easier to move the pulled group through solution, so it makes more steady progress as the molecules are separated. Hi Justin, it is right I am using umbrella pulling. Now here is another hurdle in front of me: How to select the snapshots for umbrella samples? Since the distance between two groups went higher or lower at the beginning of the pulling. For example, during the pulling simulation, the distance changes like: 0.46 0.42 0.46 0.43 0.44 0.42 0.45 0.44 0.43 0.45 0.44 0.45 0.43 0.44 0.44 0.54 0.52 0.63 0.65 0.72 0.8 0.92 1.2 1.5 (nm) . I suppose it doesn't matter which snapshots to be chosen, as long as the snapshots can indicate a good spacing, the PMF result always should be same, right? You need reasonable spacing and sufficient sampling in each window to allow for proper overlap of the umbrella potentials. -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
[gmx-users] RE: Re: Binding Energy to Binding affinity (Kd) (Justin Lemkul)
Hi Justin, I used ~20 windows to sample ~2 nm pulling. I notice that the distance between the complex being increased during the pulling but not gradually. At the distance of 0-1nm, there are 70 snapshots (the distance sometime increased sometimes decreased). At the distance of 1-2nm, there are only 30 snapshots (the distance kept increasing always). At the distance more than 3nm, the distance increased as 0.3nm of each snapshot, is it normal and reliable? You mentioned error estimate for each replicate, but what is it? How to define it? For the conversion of energy to Kd, I standardized every unit into international unit and then calculated the Kd value. Here I post my formula: $ln=2.718281828459; ## constant $cal=4186; ## convert kcal into J $R=8.3144621; #J/(mol*K) ideal gas constant $mol=6.02214179*(10**23); ## mole numbers, constant $procon=9.494/15; ## the protein concentration based on ions' concentration. mol/ml $a=$energy*$cal/$t/$R; ## $energy here is the binding energy calculated from umbrella sampling (kcal/mol) $k=$ln**$a; $kd=1/$k *$procon * (10**9); ## Kd vs Ka; unit is μM here. Thank you, Jiangfeng. On 10/1/12 4:36 AM, Du Jiangfeng (BIOCH) wrote: Dear Everyone, I have two questions about the conversion of binding energy to binding affinity. I predicted the binding energy of a protein-membrane complex by umbrella sampling (based on Justin's tutorial). After sampling, the binding energy should be the substract of (min-max) PMF. I have repeated the simulation 12 times, and then I have done umbrella samplings also 12 times, then got 12 binding energies which varies from -200 Kcal/mol to -100kcal/mol, does the value vary too much? or is it reasonable since the simulation results can be different? Are those values too huge? Without an explanation of how long your windows are and what the error estimate for each replicate is, it is impossible to answer this question. When I tried to convert the binding energy to Kd by the formula deltaG=-RTlnK, I am frustrated by the kd value. If the binding energy is -100kcal/mol, the kd is calculated as 3.35e-59 ?M. The kd is 1.77e-126 ?M when binding energy is -200kcal/mol. This is impossible. But what is going wrong? I think you are doing your calculations incorrectly (I obtain your values when using units of kcal/mol for dG but kJ/mol-K for the gas constant - note the mismatch), but even when done properly, the values are still unreasonable. -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] RE: Re: Binding Energy to Binding affinity (Kd) (Justin Lemkul)
On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote: Hi Justin, I used ~20 windows to sample ~2 nm pulling. I notice that the distance between the complex being increased during the pulling but not gradually. At the distance of 0-1nm, there are 70 snapshots (the distance sometime increased sometimes decreased). At the distance of 1-2nm, there are only 30 snapshots (the distance kept increasing always). At the distance more than 3nm, the distance increased as 0.3nm of each snapshot, is it normal and reliable? I will assume you are using a harmonic potential (umbrella) to do the pulling. In this case, your observations are totally normal. When two species interact strongly, it is harder to pull them apart, thus the spring extends further to induce a larger force before displacement occurs. As the restoring forces are overcome, it is easier to move the pulled group through solution, so it makes more steady progress as the molecules are separated. You mentioned error estimate for each replicate, but what is it? How to define it? g_wham has numerous options for statistical analysis. I would encourage you to read their full description in the g_wham paper, and at minimum, the short description in g_wham -h. For the conversion of energy to Kd, I standardized every unit into international unit and then calculated the Kd value. Here I post my formula: $ln=2.718281828459; ## constant $cal=4186; ## convert kcal into J $R=8.3144621; #J/(mol*K) ideal gas constant $mol=6.02214179*(10**23); ## mole numbers, constant $procon=9.494/15; ## the protein concentration based on ions' concentration. mol/ml This ends up being something like 633 M, which may well be correct based on size of the molecular system, but seems very odd to me. -Justin $a=$energy*$cal/$t/$R; ## $energy here is the binding energy calculated from umbrella sampling (kcal/mol) $k=$ln**$a; $kd=1/$k *$procon * (10**9); ## Kd vs Ka; unit is μM here. Thank you, Jiangfeng. On 10/1/12 4:36 AM, Du Jiangfeng (BIOCH) wrote: Dear Everyone, I have two questions about the conversion of binding energy to binding affinity. I predicted the binding energy of a protein-membrane complex by umbrella sampling (based on Justin's tutorial). After sampling, the binding energy should be the substract of (min-max) PMF. I have repeated the simulation 12 times, and then I have done umbrella samplings also 12 times, then got 12 binding energies which varies from -200 Kcal/mol to -100kcal/mol, does the value vary too much? or is it reasonable since the simulation results can be different? Are those values too huge? Without an explanation of how long your windows are and what the error estimate for each replicate is, it is impossible to answer this question. When I tried to convert the binding energy to Kd by the formula deltaG=-RTlnK, I am frustrated by the kd value. If the binding energy is -100kcal/mol, the kd is calculated as 3.35e-59 ?M. The kd is 1.77e-126 ?M when binding energy is -200kcal/mol. This is impossible. But what is going wrong? I think you are doing your calculations incorrectly (I obtain your values when using units of kcal/mol for dG but kJ/mol-K for the gas constant - note the mismatch), but even when done properly, the values are still unreasonable. -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
