Re: [gmx-users] (no subject)

I suggest check for the appropriate binding pocket. See whether the ligand relocates at some other point in protein or keep to stay away. Also check for the quality of the topology generated. On Wed, Aug 16, 2017 at 10:11 AM, wrote: > Hii Everyone > > I had performed a 100ns protein-ligand (dock

[gmx-users] (no subject)

Hii Everyone I had performed a 100ns protein-ligand (docked complex) simulation with gromacs 5.1.4. The ligand in my case is hydrogen peroxide. I have removed the PBC effect and centered the protein. I have used the following commands: gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc

[gmx-users] positioning molecule at desired location

Dear all, I want to keep a water molecule at a particular position of a protein channel. I need to pull this across the channel and observe the energy diagram by PMF. can anyone tell me how I can keep water molecules at a particular position. thank you. -- Gromacs Users mailing list * Please se

Re: [gmx-users] npt simulation error

; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 4 On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul wrote: > > > On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote: > >> Dear Sir >> >> I am trying to simulate protein_ligand complex using epsilon = 4

Re: [gmx-users] npt simulation error

On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote: Dear Sir I am trying to simulate protein_ligand complex using epsilon = 4 and it is giving the below error What is epsilon = 4? *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off out of the domain decomposit

[gmx-users] npt simulation error

Dear Sir I am trying to simulate protein_ligand complex using epsilon = 4 and it is giving the below error *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x* I have no idea how to solve this probl

[gmx-users] Doing restart

#yiv4389709560 blockquote, #yiv4389709560 div.yiv4389709560yahoo_quoted {margin-left:0 !important;border-left:1px #715FFA solid !important;padding-left:1ex !important;background-color:white;} Dear gmx users I stoped my md simulation and now i want to restart it. I use gromacs 2016.3  and issued

Re: [gmx-users] how to make molecular model with both ion channel and lipid bilayer?

Charmm-gui.org could help you. Bests, Hadi On Tue, Aug 15, 2017 at 07:55 PM, "Li, Tong" wrote: Dear all, I am trying to make a model of ion channel with cell membrane. Is there a specific software to make this? I mean just the coordination file. VMD can generate the membrane automatically, I ca

[gmx-users] how to make molecular model with both ion channel and lipid bilayer?

Dear all, I am trying to make a model of ion channel with cell membrane. Is there a specific software to make this? I mean just the coordination file. VMD can generate the membrane automatically, I can find the 'pdb' files of ion channels, but I have no idea how to combine them. Thanks all, To

[gmx-users] (Don't know if mail worked last time)Drift with groups+tabulated potential.

Dear GROMACS Community, First of all, if someone got this email twice, I am sorry. It is my first post and I was not sure if it worked. I am trying to do a simulation using a tabulated potential which forces me to use the group cut-off. I get a drift in the conserved quantity of -600KJ/mol/ns.

Re: [gmx-users] Fwd:

On 8/15/17 1:52 AM, saranya wrote: Hi, I have done protein-drug simulations for 100ns. While calculating the hydrogen bond between the protein-drug complex I am getting only 2 hydrogen bonds. The number of H-bond formation is very low I have a question about is there any influence of the drug i