Re: [gmx-users] ligand binding

On 8/7/14, 8:47 AM, Meenakshi Rajput wrote: Thank you Justin. Please tell me if emtol should be 1000 or 100 for albumin There are no hard and fast rules when running normal MD simulations. protein complex? As for emtol=1000, complex(mentioned in the tutorial) is converged in some steps and

[gmx-users] ligand binding

Thank you Justin. Please tell me if emtol should be 1000 or 100 for albumin protein complex? As for emtol=1000, complex(mentioned in the tutorial) is converged in some steps and graph plotted for potential energy shows sudden downfall. Please tell me what is the reason behind this? -- Gromacs User

Re: [gmx-users] ligand binding

On 8/6/14, 10:11 PM, Meenakshi Rajput wrote: hello I have used charmm27 force field to parametrize my protein(human serum CHARMM27 is a nucleic acid force field. The force field you're using is CHARMM22/CMAP, which is bundled (in Gromacs) in the same files. albumin,584a.a) and swiss para

[gmx-users] ligand binding

hello I have used charmm27 force field to parametrize my protein(human serum albumin,584a.a) and swiss param to provide parameters to the ligand due to which coordinates of ligand is changed and active site of protein is also completely changed. Can anybody tell me that ligand coordinates should be

Re: [gmx-users] ligand binding sampling

Generating lots of samples with the correct distribution is hard. If it wasn't, we'd all be doing something else! You may want to consider methods such as those implemented in PLUMED. Mark On Mar 16, 2014 9:42 AM, "Albert" wrote: > Hello: > > I am going to study how ligand bind to the binding p

[gmx-users] ligand binding sampling

Hello: I am going to study how ligand bind to the binding pocket of a protein from bulk environment. I noticed that De.Shaw Research used 10 us long time scale MD simulations for this purpose. I am just wondering, besides such time consuming method, is there any alternative methods in Gromacs?