[gmx-users] Protein-ligand complex simulation

Dear Gromacs User, I am running *protein ligand complex* simulation by following the Beven lab tutorial. while production run im getting two notes such as: NOTE 1 [file topol.top]: The largest charge group contains 11 atoms. Since atoms only see each other when the centers

[gmx-users] Protein ligand complex simulation

I followed the complex simulation tutorial. Minimisation for 2ns I used auto dock to dock ligand with protein. During simulation I find the ligand out of protein. Is that usual? -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list *

Re: [gmx-users] Protein-ligand complex simulation

On 1/9/17 1:58 AM, Nivedita Rai wrote: Dear Gromacs User, I am running *protein ligand complex* simulation by following the Beven lab tutorial. while production run im getting two notes such as: NOTE 1 [file topol.top]: The largest charge group contains 11 atoms. Since

Re: [gmx-users] Protein ligand complex simulation

I mean the ligand is not bonded with the protein. On Sat, 1 Apr 2017 at 6:29 PM, RAHUL SURESH wrote: > I followed the complex simulation tutorial. Minimisation for 2ns > > I used auto dock to dock ligand with protein. During simulation I find the > ligand out of protein. Is that usual? > -- > *

Re: [gmx-users] Protein ligand complex simulation

On 4/1/17 8:59 AM, RAHUL SURESH wrote: I followed the complex simulation tutorial. Minimisation for 2ns FYI there is no time during energy minimization, so you did not do "2 ns" of minimization. I used auto dock to dock ligand with protein. During simulation I find the ligand out of prot

Re: [gmx-users] Protein ligand complex simulation

Dear Justin First I apologise for the error I had made in my previous mail. It's during production. I have recentered it. The ligand is out of the protein. The ligand is not in position where I docked. On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul wrote: > > > On 4/1/17 8:59 AM, RAHUL SURESH w

Re: [gmx-users] Protein ligand complex simulation

On 4/3/17 7:56 AM, RAHUL SURESH wrote: Dear Justin First I apologise for the error I had made in my previous mail. It's during production. I have recentered it. The ligand is out of the protein. The ligand is not in position where I docked. Then watch the recentered trajectory to see what

Re: [gmx-users] Protein ligand complex simulation

The ligand is out of protein in the very first frame of production run. Then that should be my docking error.? On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul wrote: > > > On 4/3/17 7:56 AM, RAHUL SURESH wrote: > > Dear Justin > > > > First I apologise for the error I had made in my previous mail.

Re: [gmx-users] Protein ligand complex simulation

On 4/3/17 8:05 AM, RAHUL SURESH wrote: The ligand is out of protein in the very first frame of production run. Then that should be my docking error.? It sounds like your starting configuration was prepared incorrectly (however you manipulated it to prepare the system) or this is a PBC effe

Re: [gmx-users] Protein ligand complex simulation

Hi, Look at your docking result before you use it for something else. (Same goes for any computed result from any software.) Mark On Mon, 3 Apr 2017 14:06 RAHUL SURESH wrote: > The ligand is out of protein in the very first frame of production run. > Then that should be my docking error.? > >

[gmx-users] Protein-ligand complex simulation and ATBserver file

Dear all, I have started following the new tutorial and the old tutorial to carryout the simulation of JZ4 with Lysozyme. I was unable to run the cgen

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

On Tue, Dec 18, 2018 at 12:17 AM Sri Prasanth Ghanta, Doctoral Research Scholar, Biosciences, SSSIHL wrote: > Dear all, > > I have started following the new tutorial > and the old tutorial > < > http://www.bevanlab.biochem.vt.edu/Pages/Personal/

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

Dear Sir, I am running GROMACS 5.1.4 on a server. I had converted the protein(pdb2gro) using the latest GROMOS forcefield. As per your suggestion, I had downloaded the parameter files from ATB server. As per the readme file from the server (in the parameters folder), i had updated my topol.top lik

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

On Wed, Dec 19, 2018 at 4:34 AM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear Sir, > > I am running GROMACS 5.1.4 on a server. > I had converted the protein(pdb2gro) using the latest GROMOS forcefield. > As per your suggestion, I had downloaded the parameter files from

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

Dear Sir, Thanks a lot for the inputs. I tried incorporating the forcefield parameters (directory) obtained from the atbserver in the working directory. When i was trying to convert the protein.pdb to .gro, I noticed that the forcefield showed up in the menu as one included in local directory, jus

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

On Thu, Dec 20, 2018 at 10:05 AM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear Sir, > > Thanks a lot for the inputs. I tried incorporating the forcefield > parameters (directory) obtained from the atbserver in the working > directory. When i was trying to convert the p