[Chimera-users] Solvate Tool Trouble

Mike Bergman bergm310 at umn.edu
Mon Jul 25 08:16:34 PDT 2016

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. :)
Mikey Bergman

On Wed, Jul 20, 2016 at 9:58 PM, Mike Bergman <bergm310 at 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 at 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 at 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

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