[Chimera-users] How to calculate the deviation of two ligands in the same pocket

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 3 09:33:21 PDT 2013

Hi Andrés,
My previous answer still applies, but perhaps I did not give enough detail:

(1) superimpose the receptors.  You could do this with MatchMaker or command mmaker, or command match … these various methods are discussed here:

(2) then use the command "rmsd" to measure the RMSD between the two ligand positions.  This command does not move anything, and it uses the current positions whatever atoms you tell it to use.  If you specify the ligand it will calculate the RMSD of the ligand atoms only.  I can't give you the exact command because it depends on what models you have, and their residue and atom names.   

I hope this helps,

On May 31, 2013, at 12:21 PM, felipe vasquez <anfelvas at gmail.com> wrote:

> Hi Elaine,
> I want to compare two different docking poses with the same ligand and receptor. The only difference is that, in one of the receptors, it was included a water molecule. So, as a result, the ligand occupies a vey different position in the active site (approximately moved 2 angstroms and rotated 180 degrees) compared to the ligand in the first receptor (without the water molecule). Now, I want to discuss this difference in a quantitative manner, but if I try to calculate the RMSD of the entire docking poses, Chimera and other programs only take into account the receptor and not the ligand, and as a result my RMSD is 0.000. Now, if I 'cut' the ligand and save it as a different file in both cases, once I try to calculate RMSD, the original position of the ligands is lost, and I obtain a undesirable value. Is it the estimation of RMSD appropriate (informative) for evaluating the conformational change of my ligand to discuss the difference in protein-ligand interaction?
> Best regards,
> Andrés Felipe Vásquez J., MSc.
> Grupo de Fisiología Molecular
> Instituto Nacional de Salud
> Avenida calle 26 No. 51-20 - Zona 6 CAN
> Bogotá, D.C., Colombia 
> 2013/5/31 Elaine Meng <meng at cgl.ucsf.edu>
> Hi Andrés,
> The "rmsd" command calculates RMSD in the current positions, without moving any atoms to fit.  See:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
> MatchMaker  only uses the CA atoms of the protein chains in fitting and in calculating the RMSD, so the value from MatchMaker wouldn't tell you anything about the ligand.  Instead, you might use MatchMaker first to superimpose the proteins, if they aren't already superimposed, and then use the "rmsd" command to compare the resulting two ligand positions.
> Explanation of the different superposition methods in Chimera and how they work:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> 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 May 30, 2013, at 12:43 PM, felipe vasquez <anfelvas at gmail.com> wrote
> > Hi,
> > I am working on the modeling of one ligand in a native and mutant receptor. The ligand occupies different positions in the binding cavity, and I am interested in estimate this difference. However, if RMSD is calculated via MatchMaker, the ligand in mutant receptor (non-reference) is moved from its original position to try to minimize the deviation compared to ligand in native receptor (reference). How can I calculate the difference in the ligand position between the two receptors, in an appropriate manner?

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