Hey there. I am having trouble with the solvate tool. I am using a dimeric model (PDB ID: 2Q1E) that isn't attached. Every time I try to solvate (model TIP3PBOX), it squishes the dimer together. I tried different angstrom box sizes - 3, 5, 10, 20. Running the simulation with them overlaid wouldn't give me any useful data as I'm looking for the changes in the dimer interface. Is there a way I can stop it from doing this? Should I use a different solvate method like Shell? Thanks. Sincerely, Mikey Bergman
Hi Mikey, I could not reproduce this problem. I opened 2Q1E, started Solvate, used box TIP3PBOX size 5 with “Remove existing ions/solvent” turned on, then added hydrogens with default settings (one is automatically prompted to add hydrogens if they are missing), and several seconds later got the structure in a box of solvent. Then I opened another copy of 2Q1E to see if anything had changed. I see that Solvate does change the coordinates but only as a rigid body, i.e. although the second copy was in a different place, when I superimposed the two copies of the structure with matchmaker they looked exactly the same. So, I guess make sure it’s not simply your viewing angle that makes it seem like something changed. If you are sure the dimer changed, then you should use Help… Report a Bug (which would tell us your exact version of Chimera and operating system) and attach the structure you are trying to solvate unless it’s exactly the same as PDB entry 2Q1E. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 20, 2016, at 11:42 AM, Mike Bergman <bergm310@umn.edu> wrote:
Hey there. I am having trouble with the solvate tool. I am using a dimeric model (PDB ID: 2Q1E) that isn't attached. Every time I try to solvate (model TIP3PBOX), it squishes the dimer together. I tried different angstrom box sizes - 3, 5, 10, 20. Running the simulation with them overlaid wouldn't give me any useful data as I'm looking for the changes in the dimer interface. Is there a way I can stop it from doing this? Should I use a different solvate method like Shell? Thanks. Sincerely, Mikey Bergman
Thank you for looking into this for me Elaine. I understand that the structure itself doesn't change. Also, the file is actually composed of two identical monomers, so I would hope they align well :) For the simulation, it would be nice if they remain locked in their coordinates so that the changes in the dimeric interface can be observed. If that's not possible when solvating, then I'll have to find a different approach for my inquiry. I apologize if my question wasn't very clear the first time. I'm very new to molecular dynamics and have been trying to teach myself as I go. CHIMERA has proven extremely user friendly and I really appreciate that, as well as the support you offer. So my question really is how to lock the position/coordinates of the monomers when solvating. Thank you very much for your time. Sincerely, Mikey Bergman On Wed, Jul 20, 2016 at 4:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Mikey, I could not reproduce this problem.
I opened 2Q1E, started Solvate, used box TIP3PBOX size 5 with “Remove existing ions/solvent” turned on, then added hydrogens with default settings (one is automatically prompted to add hydrogens if they are missing), and several seconds later got the structure in a box of solvent. Then I opened another copy of 2Q1E to see if anything had changed. I see that Solvate does change the coordinates but only as a rigid body, i.e. although the second copy was in a different place, when I superimposed the two copies of the structure with matchmaker they looked exactly the same.
So, I guess make sure it’s not simply your viewing angle that makes it seem like something changed.
If you are sure the dimer changed, then you should use Help… Report a Bug (which would tell us your exact version of Chimera and operating system) and attach the structure you are trying to solvate unless it’s exactly the same as PDB entry 2Q1E. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 20, 2016, at 11:42 AM, Mike Bergman <bergm310@umn.edu> wrote:
Hey there. I am having trouble with the solvate tool. I am using a dimeric model (PDB ID: 2Q1E) that isn't attached. Every time I try to solvate (model TIP3PBOX), it squishes the dimer together. I tried different angstrom box sizes - 3, 5, 10, 20. Running the simulation with them overlaid wouldn't give me any useful data as I'm looking for the changes in the dimer interface. Is there a way I can stop it from doing this? Should I use a different solvate method like Shell? Thanks. Sincerely, Mikey Bergman
Hey again Elaine. Just wanted to let you know I figured out what my problem was. I had apparently split the model into 2. When I re-opened the PDB instead of my own file, the problem was resolved. Thank you for your help. :) Sincerely, Mikey Bergman On Wed, Jul 20, 2016 at 9:58 PM, Mike Bergman <bergm310@umn.edu> wrote:
Thank you for looking into this for me Elaine. I understand that the structure itself doesn't change. Also, the file is actually composed of two identical monomers, so I would hope they align well :) For the simulation, it would be nice if they remain locked in their coordinates so that the changes in the dimeric interface can be observed. If that's not possible when solvating, then I'll have to find a different approach for my inquiry.
I apologize if my question wasn't very clear the first time. I'm very new to molecular dynamics and have been trying to teach myself as I go. CHIMERA has proven extremely user friendly and I really appreciate that, as well as the support you offer. So my question really is how to lock the position/coordinates of the monomers when solvating. Thank you very much for your time. Sincerely, Mikey Bergman
On Wed, Jul 20, 2016 at 4:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Mikey, I could not reproduce this problem.
I opened 2Q1E, started Solvate, used box TIP3PBOX size 5 with “Remove existing ions/solvent” turned on, then added hydrogens with default settings (one is automatically prompted to add hydrogens if they are missing), and several seconds later got the structure in a box of solvent. Then I opened another copy of 2Q1E to see if anything had changed. I see that Solvate does change the coordinates but only as a rigid body, i.e. although the second copy was in a different place, when I superimposed the two copies of the structure with matchmaker they looked exactly the same.
So, I guess make sure it’s not simply your viewing angle that makes it seem like something changed.
If you are sure the dimer changed, then you should use Help… Report a Bug (which would tell us your exact version of Chimera and operating system) and attach the structure you are trying to solvate unless it’s exactly the same as PDB entry 2Q1E. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 20, 2016, at 11:42 AM, Mike Bergman <bergm310@umn.edu> wrote:
Hey there. I am having trouble with the solvate tool. I am using a dimeric model (PDB ID: 2Q1E) that isn't attached. Every time I try to solvate (model TIP3PBOX), it squishes the dimer together. I tried different angstrom box sizes - 3, 5, 10, 20. Running the simulation with them overlaid wouldn't give me any useful data as I'm looking for the changes in the dimer interface. Is there a way I can stop it from doing this? Should I use a different solvate method like Shell? Thanks. Sincerely, Mikey Bergman
Hi MIkey, Short answer is that you can’t, but I don’t think it matters. I will try to explain: I didn’t mean that the two monomers are identical to each other (although they might be), I meant that the whole dimer structure is exactly the same before and after solvation, except just moved as a rigid body. Thus the interface is not changed from the original structure, so you could now use the solvated structure as the basis for comparison. Solvation is done via Ambertools and there is no option to keep the coordinates exactly the same. Keep in mind that your dimer may also move around during the simulation, so you’d have to think about whether that is the case and compensate for it before doing any comparisons of the interface with and among your simulation results. I.e. any comparison may require processing the trajectory to remove rotation and translation of the dimer as much as possible, and/or always first matching (superimposing) the dimer within the two snapshots you are trying to compare. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 20, 2016, at 7:58 PM, Mike Bergman <bergm310@umn.edu> wrote:
Thank you for looking into this for me Elaine. I understand that the structure itself doesn't change. Also, the file is actually composed of two identical monomers, so I would hope they align well :) For the simulation, it would be nice if they remain locked in their coordinates so that the changes in the dimeric interface can be observed. If that's not possible when solvating, then I'll have to find a different approach for my inquiry.
I apologize if my question wasn't very clear the first time. I'm very new to molecular dynamics and have been trying to teach myself as I go. CHIMERA has proven extremely user friendly and I really appreciate that, as well as the support you offer. So my question really is how to lock the position/coordinates of the monomers when solvating. Thank you very much for your time. Sincerely, Mikey Bergman
On Wed, Jul 20, 2016 at 4:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Mikey, I could not reproduce this problem.
I opened 2Q1E, started Solvate, used box TIP3PBOX size 5 with “Remove existing ions/solvent” turned on, then added hydrogens with default settings (one is automatically prompted to add hydrogens if they are missing), and several seconds later got the structure in a box of solvent. Then I opened another copy of 2Q1E to see if anything had changed. I see that Solvate does change the coordinates but only as a rigid body, i.e. although the second copy was in a different place, when I superimposed the two copies of the structure with matchmaker they looked exactly the same.
So, I guess make sure it’s not simply your viewing angle that makes it seem like something changed.
If you are sure the dimer changed, then you should use Help… Report a Bug (which would tell us your exact version of Chimera and operating system) and attach the structure you are trying to solvate unless it’s exactly the same as PDB entry 2Q1E. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 20, 2016, at 11:42 AM, Mike Bergman <bergm310@umn.edu> wrote:
Hey there. I am having trouble with the solvate tool. I am using a dimeric model (PDB ID: 2Q1E) that isn't attached. Every time I try to solvate (model TIP3PBOX), it squishes the dimer together. I tried different angstrom box sizes - 3, 5, 10, 20. Running the simulation with them overlaid wouldn't give me any useful data as I'm looking for the changes in the dimer interface. Is there a way I can stop it from doing this? Should I use a different solvate method like Shell? Thanks. Sincerely, Mikey Bergman
participants (2)
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Elaine Meng -
Mike Bergman