Re: [gmx-users] Homology model refinement

Hi Mijiddorj, My target protein size is around 250 residues. It's pretty small and i don't have issue with time. Can you please let me know the actual command line for cluster analysis? Regards! On Thu, Dec 22, 2016 at 12:59 AM, Mijiddorj Batsaikhan < b.mijidd...@gmail.com> wrote: > Hi, > >

Re: [gmx-users] Homology model refinement

Hi, What is your target structure size? If you want to perform explicit solvent simulation for bigger protein, it may be time-consuming simulation. My suggestion is that you can run simulation implicitly, it helps you remove some bad contacts. Then, you can make cluster analysis and find

Re: [gmx-users] Homology model refinement

Hi Mark, Thanks for your response. I did for simulation for both the systems 1. only protein 2. protein with co-factor. By the way, I'm not pretty sure, but I'm relying on rmsd of C-alpha to evaluate the structure's stability. In both the cases, the rmsd range was highly wide ~3-6 nm. Then i

Re: [gmx-users] Homology model refinement

Hi, On Thu, Dec 22, 2016 at 5:19 PM Amir Zeb wrote: > Hi Mark, > > I want to refine the model for any bad contact if the structure has. So, do you expect the structure to be stable in the absence of the other things? That tells you whether you need to attempt refinement

Re: [gmx-users] Homology model refinement

Hi Mark, I want to refine the model for any bad contact if the structure has. This article support the simulation of any homology model after its creation by homology modeling approach " https://www.ncbi.nlm.nih.gov/pubmed/22513870?dopt=Abstract;. Do you please think that there is no need to

Re: [gmx-users] Homology model refinement

Hi, What us the purpose in doing MD on the homology model? That'll tell you whether you need a model with the other parts. Mark On Thu, 22 Dec 2016 16:51 Amir Zeb wrote: > Hello, > > I have created a homology model for a protein, where the seq. identity > between the

[gmx-users] Homology model refinement

Hello, I have created a homology model for a protein, where the seq. identity between the template and target is 40%. The template structure also contains co-factor and an inhibitor in bound form means it is a complex. I'll have to define the ligand binding site in target (homology model) based