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

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,

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

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

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 > < >

[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

Re: [gmx-users] protein -ligand complex dissociating during simulation

Dear Rahul and Justin Thanks for the suggestion, I will check the parameterisation once more. Regards Sneha On Sat, Jul 22, 2017 at 7:05 AM, RAHUL SURESH wrote: > On Sat, 22 Jul 2017 at 2:47 AM, Justin Lemkul wrote: > > > > > > > On 7/21/17 10:56 AM,

Re: [gmx-users] protein -ligand complex dissociating during simulation

On Sat, 22 Jul 2017 at 2:47 AM, Justin Lemkul wrote: > > > On 7/21/17 10:56 AM, RAHUL SURESH wrote: > > It sounds like some internal dihedral problem. Request you, check on it. > > > > How did you deduce that? Dear Justin I faced the similar kind of problem. Visualisation Of

Re: [gmx-users] protein -ligand complex dissociating during simulation

It sounds like some internal dihedral problem. Request you, check on it. On Fri, 21 Jul 2017 at 6:54 PM, Sneha Vishwanath < snehavishwanat...@gmail.com> wrote: > @ Justin: I have re-imaged the trajectory with trjconv using and still the > ligand dissociates from one of the chain but remain

Re: [gmx-users] protein -ligand complex dissociating during simulation

On 7/21/17 8:56 AM, Sneha Vishwanath wrote: Dear all I am simulating a dimeric protein, with each subunit bound to a small molecule. During the simulation, one of the ligands is dissociating from the chain and moving all around the chain while the same ligand remains bound to the chain during

Re: [gmx-users] protein -ligand complex dissociating during simulation

Hey! You might want to constrain the bond between the 2 protein chains. G *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology 174 Frelinghuysen Road, Piscataway, NJ 08854 Phone: +16092162254 On Fri, Jul 21, 2017 at 8:56 AM,

Re: [gmx-users] protein ligand complex Energy Minimisation

Hi, On Fri, May 5, 2017 at 1:44 PM Patel, Hershna wrote: > > Dear Gromacs users > > > I am trying to do energy minimisation of a protein-ligand complex. When > visualising the output trajectory and .gro file, the structure of the > ligand becomes distorted. The same thing

Re: [gmx-users] protein ligand complex Energy Minimisation

HI, It will be very helpful if you can provide the log file and I think this is a note by gromacs and not a warning. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] protein ligand complex Energy Minimisation

Dear Gromacs users I am trying to do energy minimisation of a protein-ligand complex. When visualising the output trajectory and .gro file, the structure of the ligand becomes distorted. The same thing happens when constraining all-bonds during EM. After running grompp, there is this note:

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

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

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

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

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

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

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

[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 mdrun errors

On 3/17/17 12:43 PM, Vignesh Waran wrote: respected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the

[gmx-users] protein-ligand complex mdrun errors

espected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the problem? pls tell me sir GROMACS: gmx

[gmx-users] protein-ligand complex mdrun errors

espected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the problem? pls tell me sir GROMACS: gmx

[gmx-users] protein-ligand complex mdrun errors

respected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the problem? pls tell me sir GROMACS: gmx

Re: [gmx-users] Protein-Ligand Complex MD simulation : Number of Hydrogen bond ; Options to Choose

Hi, Asking for "the number of hydrogen bonds" is ill formed. Between what and what? Mark On Wed, 25 Jan 2017 09:48 Adarsh V. K. wrote: > Dear all, > > Protein-ligand complex MD simulation using Gromacs 5.1.4 (Drug discovery) > > Can you please tell me command for

[gmx-users] Protein-Ligand Complex MD simulation : Number of Hydrogen bond ; Options to Choose

Dear all, Protein-ligand complex MD simulation using Gromacs 5.1.4 (Drug discovery) Can you please tell me command for Number of Hydrogen bond plot? It is # gmx hbond... But what option we have to choose, apart from Ligand (13) Is it (option after the command), protein protein-H side chain

Re: [gmx-users] Protein-Ligand Complex MD simulation ; Command for Number of Hydrogen bond plo

On 1/13/17 10:51 PM, Adarsh V. K. wrote: Dear all, Protein-ligand complex MD simulation using Gromacs 5.1.4 Can you please tell me command for Number of Hydrogen bond plot? and Other interactions between protein and ligand? gmx hbond calculates hydrogen bonds. Select the protein and the

[gmx-users] Protein-Ligand Complex MD simulation ; Command for Number of Hydrogen bond plo

Dear all, Protein-ligand complex MD simulation using Gromacs 5.1.4 Can you please tell me command for Number of Hydrogen bond plot? and Other interactions between protein and ligand? Regards, Adarsh V. K. -- Gromacs Users mailing list * Please search the archive at

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.

[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

Re: [gmx-users] Protein-Ligand Complex MD simulation: Restrain protein alone or Restrain both protein and ligand during simulation?

Hello, You may follow " http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/ " Everything will go fine Good luck Amir On Wed, Dec 21, 2016 at 8:50 PM, Adarsh V. K. wrote: > Dear all, > > We have a 419 amino acid long protein and planned

[gmx-users] Protein-Ligand Complex MD simulation: Restrain protein alone or Restrain both protein and ligand during simulation?

Dear all, We have a 419 amino acid long protein and planned Protein-ligand complex MD simulation using Gromacs 5.1.4 to check. 1. What sought of MD simulation we have to perform?. 2. Restrain protein alone or Restrain both protein and ligand during simulation?. 3. What is the exact command

[gmx-users] Protein-Ligand Complex MD simulation

Dear all, We have a 419 amino acid long protein and planned Protein-ligand complex MD simulation using Gromacs 5.1.4 to check. —Whether the protein and inhibitor complex stable —Did the inhibitor remain in the active site pocket or did it fall out during the simulation —What factors

[gmx-users] Protein-Ligand Complex MD simulation

We have a 419 amino acid long protein and planned for Protein-ligand complex MD simulation using Gromacs 5.1.4 to check. —Whether the protein and inhibitor complex stable —Did the inhibitor remain in the active site pocket or did it fall out during the simulation —What

[gmx-users] Protein-Ligand Complex MD simulation

Dear all, We have a 419 amino acid long proteing and planned Protein-ligand complex MD simulation using Gromacs 5.1.4 to check. —Whether the protein and inhibitor complex stable —Did the inhibitor remain in the active site pocket or did it fall out during the simulation —What factors contributed

Re: [gmx-users] protein ligand complex MD simulation

Hi Ashan, This (from the manual, section 4.3.5) https://dl.dropboxusercontent.com/u/50317782/distance_restraints_gromacs.png or this http://www.gromacs.org/Documentation/How-tos/Distance_Restraints will help. Best, Sajeewa On Thu, Dec 8, 2016 at 5:35 AM, ashan dayananda

[gmx-users] protein ligand complex MD simulation

Dear Researches, i'm currently doing a MD simulation of a protein and a ligand.i want to restrain the distance of two amino acids in the active site to 4.0 angstroms. can any one help me to perform this task. Thank you Regards Ashna -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Protein-Ligand complex MD

...@gromacs.org Subject: Re: [gmx-users] Protein-Ligand complex MD On 2/24/16 11:39 PM, Adamu, Aliyu wrote: > Hello, > > I am running the Gromacs tutorial for Protein-Ligand complex described by > Justin Lemkul. I am using Gromacs 4.6.7 on ubuntu PC platform. I successfully > ran all the

Re: [gmx-users] Protein-Ligand complex MD

On 2/24/16 11:39 PM, Adamu, Aliyu wrote: Hello, I am running the Gromacs tutorial for Protein-Ligand complex described by Justin Lemkul. I am using Gromacs 4.6.7 on ubuntu PC platform. I successfully ran all the commands until the equilibration stage. the 'grompp -f nvt.mdp -c em.gro -p

Re: [gmx-users] Protein-Ligand complex MD

there are lots of threads in this mailing list regarding and in gromacs doc also it is mentioned.please go though those you will get an idea http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PM E_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_

[gmx-users] Protein-Ligand complex MD

Hello, I am running the Gromacs tutorial for Protein-Ligand complex described by Justin Lemkul. I am using Gromacs 4.6.7 on ubuntu PC platform. I successfully ran all the commands until the equilibration stage. the 'grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr' command was

Re: [gmx-users] Protein-Ligand complex Implicit simulation

Please remember to use a proper subject line and don't reply to the whole digest. On 5/20/15 9:54 AM, sunita gupta wrote: Thanks Justin for your reply Below is the file where I added h1 parameters in gbsa.itp...In the same way I added the parameters for all the possible atomtypes from gaff

[gmx-users] Protein-Ligand complex Implicit simulation

Hello Everyone, I am trying to do protein-ligand complex simulation with implicit solvent parameters using gromacs. As, ligand parameters are not present in gbsa.itp, I added all the possible atomtypes and their van der wall radii from gaff ff and also managed to get get the HCT paremeters.

Re: [gmx-users] Protein-Ligand complex Implicit simulation

On 5/18/15 3:35 PM, sunita gupta wrote: Hello Everyone, I am trying to do protein-ligand complex simulation with implicit solvent parameters using gromacs. As, ligand parameters are not present in gbsa.itp, I added all the possible atomtypes and their van der wall radii from gaff ff and also

Re: [gmx-users] Protein+ligand complex

On 5/15/15 1:36 AM, Kashif wrote: I have done MD simulation of my protein and ligand docked complex. My protein is having 900 amino acids. When I use g_rms to analyse rmsd, the graph is too short. Currently I am simulating my protein for 5 ns. Should I increase my ns for such big protein and

[gmx-users] Protein+ligand complex

Greetings of the day, Can I use nvt.mdp and npt.mdp parameter file given in tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html) for my 5 ns production run? As the tutorial shows 100 ps nvt and npt equilibration and 1000 ps (1 ns) MD Simulation

[gmx-users] protein-ligand complex fatal error

hi i just want to run mdrun -v deffnm nvt i run every command in this tutorials http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html but at the end i got two errors : There are: 247500 Atoms Charge group distribution at step 0: 20986 20508 20732 20838

Re: [gmx-users] protein-ligand complex fatal error

On 12/12/14 9:19 AM, Yaser Hosseini wrote: hi i just want to run mdrun -v deffnm nvt i run every command in this tutorials http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html but at the end i got two errors : There are: 247500 Atoms Charge group

Re: [gmx-users] protein-ligand complex fatal error

On 12/8/14 2:36 PM, Yaser Hosseini wrote: hi gromacs users i want to run Protein-Ligand Complex but when i want to run this command : mdrun -deffnm nvt i got this error Fatal error: 4 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition

Re: [gmx-users] protein-ligand complex by gromacs

did you center everything, or are you just looking at it in VMD? Gesendet:Montag, 08. September 2014 um 18:30 Uhr Von:Mahboobeh Eslami mahboobeh.esl...@yahoo.com An:gmx-us...@gromacs.org gmx-us...@gromacs.org Betreff:[gmx-users] protein-ligand complex by gromacs hi GMX users i have simulated

[gmx-users] protein-ligand complex by gromacs

hi GMX users i have simulated the protein-ligand complex by gromacs. I've repeated the simulation twice but i have get very different results. in one of the simulations ligand separated from protein and stayed in the center of box. I've checked all of the input files and the steps , but I did

Re: [gmx-users] protein-ligand complex by gromacs

On 9/8/14 12:30 PM, Mahboobeh Eslami wrote: hi GMX users i have simulated the protein-ligand complex by gromacs. I've repeated the simulation twice but i have get very different results. in one of the simulations ligand separated from protein and stayed in the center of box. I've checked

Re: [gmx-users] Protein-ligand complex energy minimization

Thank you Justin. With regards, Indu On Tue, Aug 12, 2014 at 5:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/12/14, 4:58 AM, Indu Kumari wrote: Grompp terminated and shows following warning and notes: NOTE 1 [file topol.top, line 57]: System has non-zero total charge: -0.675997

Re: [gmx-users] protein-ligand complex

dear justin I thank you for your friendly guide Can I assume some of torsion steady and don't change them for getting results better of docking  ? can i reduce rotatable bonds for my ligand in docking process then do MD simulation? if i reduce rotatable bonds, i will get much better results of

Re: [gmx-users] protein-ligand complex

On 1/18/14, 3:14 AM, Mahboobeh Eslami wrote: dear justin I thank you for your friendly guide Can I assume some of torsion steady and don't change them for getting results better of docking ? can i reduce rotatable bonds for my ligand in docking process then do MD simulation? if i reduce

Re: [gmx-users] protein-ligand complex

dear justin i have another question Can the increasing of  MD simulation time improve docking results?  can the increasing of  MD simulation time create the experimental conformation of the ligand in the active site of the protein or close to it? I'm sorry if my question has problem grammar I am

Re: [gmx-users] protein-ligand complex

dear justin thanks a lot if i use flexible receptor in docking process, must i  change  the coordinates of the protein as initial configuration  in the MD simulation? Sincerely On Friday, January 17, 2014 4:42 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/17/14, 3:15 AM, Mahboobeh

Re: [gmx-users] protein-ligand complex

dear justin Some articles mentioned that the  protein simulation in water before docking can improve the docking results. Do you think that this is true? Thank you for your helpful answers On Friday, January 17, 2014 6:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/17/14, 9:54 AM,

Re: [gmx-users] protein-ligand complex

On 1/17/14, 10:23 AM, Mahboobeh Eslami wrote: dear justin Some articles mentioned that the protein simulation in water before docking can improve the docking results. Do you think that this is true? Yes. -Justin -- == Justin A. Lemkul,

[gmx-users] protein-ligand complex

hi GMX user please help me i want to simulated a protein-ligand complex. This complex has previously been studied experimentally. I  draw and opt this ligand by Gaussian software. i get the native protein of RCSB. i dock my ligand in the active site of the protein and select the best pose.

Re: [gmx-users] protein-ligand complex

On 1/16/14, 9:51 AM, Mahboobeh Eslami wrote: hi GMX user please help me i want to simulated a protein-ligand complex. This complex has previously been studied experimentally. I draw and opt this ligand by Gaussian software. i get the native protein of RCSB. i dock my ligand in the active

Re: [gmx-users] protein-ligand complex

dear justin I sincerely thank you Can I use flexible receptor in docking process and then do the MD simulation? In this case, will the coordinates of the protein  in MD simulation be changed? best wishes for you On Thursday, January 16, 2014 11:26 PM, Justin Lemkul jalem...@vt.edu wrote: