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

Re: [gmx-users] RMSD analysis and stability

On 9/15/19 7:27 AM, Bratin Kumar Das wrote: You can see the radius of gyration, number of hydrogen bond, native contact etc for assessing the stability Overall, "stability" implies persistence of important interactions (really it implies knowledge of free energy of the system, but

Re: [gmx-users] RMSD analysis and stability

You can see the radius of gyration, number of hydrogen bond, native contact etc for assessing the stability On Sun 15 Sep, 2019, 4:32 PM Quin K, wrote: > Thank you! > What else should I be looking for? > [image: mailcastr branding] Sent with Mailcastr > < >

Re: [gmx-users] RMSD analysis and stability

Thank you! What else should I be looking for? [image: mailcastr branding] Sent with Mailcastr On Sun, Sep 15, 2019 at 4:16 PM Justin Lemkul wrote: > > > On 9/15/19 5:30 AM, Quin K wrote: > > Hi everyone!

Re: [gmx-users] RMSD analysis and stability

On 9/15/19 5:30 AM, Quin K wrote: Hi everyone! I have done a MD simulation for a protein structure at 310K (100ns) this is the RMSD at around 65 ns kindly comment on the stability. Will I have to rerun the MD? Kindly let me know how to decide stability by analyzing RMSD. RMSD alone is

[gmx-users] RMSD analysis and stability

Hi everyone! I have done a MD simulation for a protein structure at 310K (100ns) this is the RMSD at around 65 ns kindly comment on the stability. Will I have to rerun the MD? Kindly let me know how to decide stability by analyzing RMSD. For backbone

Re: [gmx-users] RMSD analysis

On 6/6/17 4:01 PM, RAHUL SURESH wrote: Dear Justin I think I have confused so much. Let me try to put it in simple way. 1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of monomer(just protein) to explain stability? RMSD may be an indicator of something going on but by

Re: [gmx-users] RMSD analysis

Dear Justin I think I have confused so much. Let me try to put it in simple way. 1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of monomer(just protein) to explain stability? 2. Time step of monomer(just protein) simulation is 150ns and protein-ligand complex is 50ns. In

Re: [gmx-users] RMSD analysis

On 6/6/17 1:11 PM, RAHUL SURESH wrote: Dear Justin Thank you. I am considering Rmsd rmsf rg as just supplementary analysis for my study. My aim to analyse conformational change in protein. I would like to bring a note on protein stability after ligand binding. I don't know to which part of

Re: [gmx-users] RMSD analysis

Dear Justin Thank you. I am considering Rmsd rmsf rg as just supplementary analysis for my study. My aim to analyse conformational change in protein. I would like to bring a note on protein stability after ligand binding. I don't know to which part of monomer I can compare the rmsd of complex

Re: [gmx-users] RMSD analysis

On 6/6/17 2:12 AM, RAHUL SURESH wrote: Dear Users *Exp procedure:* I have simulated the protein monomer for 150ns. Using the 150ns conformer, ligand is docked to the protein using autodock and the simulation is carried out for 50ns. *Analysis:* Is it possible to compare my RMSD, RMSF, ROG

[gmx-users] RMSD analysis

Dear Users *Exp procedure:* I have simulated the protein monomer for 150ns. Using the 150ns conformer, ligand is docked to the protein using autodock and the simulation is carried out for 50ns. *Analysis:* Is it possible to compare my RMSD, RMSF, ROG analysis of complex system with that of