Re: [gmx-users] RMSD analysis of protein-ligand complex

Thank you Your advice is very helpful I will try to reparametrize the molecule, which I think is a better strategy. On Sun, Oct 6, 2019 at 6:38 AM Justin Lemkul wrote: > > > On 10/5/19 1:58 PM, Quin K wrote: > > Thank you. > > > > I examined the trajectory using VMD and noted that ligand had

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 1:58 PM, Quin K wrote: Thank you. I examined the trajectory using VMD and noted that ligand had come out of the binding site and is running around. How is this possible? I have used the guidelines in mdtutorials.com to set up the system. However it's worth noting that there was a

Re: [gmx-users] RMSD analysis of protein-ligand complex

Thank you. I examined the trajectory using VMD and noted that ligand had come out of the binding site and is running around. How is this possible? I have used the guidelines in mdtutorials.com to set up the system. However it's worth noting that there was a power failure around the same time

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 11:59 AM, Quin K wrote: Thank you. I got following when I analysed Ligand RMSD protein backbone as east square fit. Graph Can you please comment why there's high fluctuation after like 23 ns? What could this mean? Watch the

Re: [gmx-users] RMSD analysis of protein-ligand complex

Thank you. I got following when I analysed Ligand RMSD protein backbone as east square fit. Graph Can you please comment why there's high fluctuation after like 23 ns? What could this mean? Thanks Regards! On Sat, Oct 5, 2019 at 9:08 PM Justin

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 11:36 AM, Quin K wrote: OK thanks. What should I pick for least square fit in following instances for example. *RMSD of* 1. protein backbone+ligand 2. protein backbone 3. lingad only I've already answered that. And again, it always depends on the question you are asking. You

Re: [gmx-users] RMSD analysis of protein-ligand complex

OK thanks. What should I pick for least square fit in following instances for example. *RMSD of* 1. protein backbone+ligand 2. protein backbone 3. lingad only On Sat, Oct 5, 2019 at 8:56 PM Justin Lemkul wrote: > > > On 10/5/19 11:24 AM, Quin K wrote: > > Thank you! > > How important is the

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 11:24 AM, Quin K wrote: Thank you! How important is the least square fit in these RMSD calculations? Very; it determines how to interpret the result. Or should I just pick system for least square fit all time? You should never pick "System" for a fit. -Justin On Sat, Oct

Re: [gmx-users] RMSD analysis of protein-ligand complex

Thank you! How important is the least square fit in these RMSD calculations? Or should I just pick system for least square fit all time? On Sat, Oct 5, 2019 at 8:45 PM Justin Lemkul wrote: > > > On 10/5/19 11:11 AM, Quin K wrote: > > To see if complex is stable and to see how it fluctuate in

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 11:11 AM, Quin K wrote: To see if complex is stable and to see how it fluctuate in the binding site. Stability of the complex can mean multiple things. If you want to show that the protein structure is stable in the presence of the ligand, you would compute the RMSD of the

Re: [gmx-users] RMSD analysis of protein-ligand complex

To see if complex is stable and to see how it fluctuate in the binding site. On Sat, Oct 5, 2019 at 8:33 PM Justin Lemkul wrote: > > > On 10/5/19 10:53 AM, Quin K wrote: > > Hi, > > > > *What should I pick for RMSD analysis of protein ligand complex? * > > *What other analysis can be done for

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 10:53 AM, Quin K wrote: Hi, *What should I pick for RMSD analysis of protein ligand complex? * *What other analysis can be done for protein ligand complex? * Following are the options I have for least square fit and for RMSD calculation. MPPA is the ligand I used. Group 0 (

[gmx-users] RMSD analysis of protein-ligand complex

Hi, *What should I pick for RMSD analysis of protein ligand complex? * *What other analysis can be done for protein ligand complex? * Following are the options I have for least square fit and for RMSD calculation. MPPA is the ligand I used. Group 0 ( System) has 50085 elements Group