Re: [gmx-users] Protein ligand simulation topology

On 10/8/19 7:30 AM, DEEPANSHU SINGLA wrote: Respected sir/mam, While doing the simulation of my protein with a ligand I received the following error: Fatal Error: No line with moleculetype 'SOL' found in the [molecules] section of the 'topol.top' Molecule section of my topology file is as f

[gmx-users] Protein ligand simulation topology

Respected sir/mam, While doing the simulation of my protein with a ligand I received the following error: Fatal Error: No line with moleculetype 'SOL' found in the [molecules] section of the 'topol.top' Molecule section of my topology file is as follows: [molecules] ; Compound#mols Prot

[gmx-users] Protein ligand simulation

Respected sir/mam, During ligand topology generation I received the following error: Please be sure to use the same version of CGenFF in your simulation that was used during parameter generation: --version of CGenFF detected in charmm36-mar2019.ff/forcefield.doc : 4.1 WARNING: cGenFF versions ar

Re: [gmx-users] Protein ligand simulation

On 10/1/19 3:39 AM, DEEPANSHU SINGLA wrote: I am trying to learn protein ligand simulation. I tried to follow the steps for lysozyme using the GROMACS tutorial. I received the following error: *ERROR 1 {file jz4.itp, line 183]:* * No default Proper Dih. types* *ERROR 2 [file jz4.itp, line 1

Re: [gmx-users] Protein ligand simulation

you should follow steps from protein-Ligand simulation. Write in google " www.bevanlab.biochem.vt.edu › justin › gmx-tutorials › complex_old ". Take coordinates of JZ4 from PRODRG.

[gmx-users] Protein ligand simulation

I am trying to learn protein ligand simulation. I tried to follow the steps for lysozyme using the GROMACS tutorial. I received the following error: *ERROR 1 {file jz4.itp, line 183]:* * No default Proper Dih. types* *ERROR 2 [file jz4.itp, line 194]:* * No default Proper Dih. types* *Fatal err

Re: [gmx-users] Protein ligand simulation

First of all take coordinates of ligand from online available resources mentioned in protocol of protein ligand simulation and exactly follow the same you will get simulation run Regards Najam On Sat, Sep 28, 2019, 2:38 PM DEEPANSHU SINGLA wrote: > I am trying to learn protein ligand simulatio

[gmx-users] Protein ligand simulation

I am trying to learn protein ligand simulation. I tried to follow the steps for lysozyme using the GROMACS tutorial. I received the following error: *ERROR 1 {file jz4.itp, line 183]:* * No default Proper Dih. types* *ERROR 2 [file jz4.itp, line 194]:* * No default Proper Dih. types* *Fatal err

[gmx-users] protein-ligand simulation problem

Hi Gromacs Users, I am trying to protein-ligand simulation where I have 12 protein and 12 ligand molecules. Minimization step went perfectly well and the system got minimized less than 2 steps. However, it is becoming unstable once I am trying to do real simulation. I am trying to equilibrate

Re: [gmx-users] PROTEIN-LIGAND SIMULATION

On 2/17/17 8:43 AM, Subashini .K wrote: Hi gromacs users, In order to calculate binding energy of single protein inhibitor complex through simulations, how long should we run the calculations? Is 2ns sufficient? The answer to this question is always: "have the observables of interest c

[gmx-users] PROTEIN-LIGAND SIMULATION

Hi gromacs users, In order to calculate binding energy of single protein inhibitor complex through simulations, how long should we run the calculations? Is 2ns sufficient? How to obtain results and plot time (in ps) along x-axis and binding energy (kJ/mol)along y-axis? Had completed two e

[gmx-users] PROTEIN LIGAND SIMULATION DYNAMICS

Hi Gromacs users, I am new to simulation dynamics. On what basis do we add water molecules to the protein ligand complex? Should we ensure that the system is fully solvated? Or, can we consider simulation without solvent (water molecules)? Thanks, Subashini.K -- Gromacs Users mailin

Re: [gmx-users] Protein Ligand simulation

On 5/6/16 2:26 PM, Alex Mathew wrote: Greetings to all ! i have completed Protein Ligand simulation as per the tutorial,my aim to proof that ligand A inhibit Ligand B -what are the possible analysis i can perform i have done the following RMSD - to see the stability of protein with ligands

[gmx-users] Protein Ligand simulation

Greetings to all ! i have completed Protein Ligand simulation as per the tutorial,my aim to proof that ligand A inhibit Ligand B -what are the possible analysis i can perform i have done the following RMSD - to see the stability of protein with ligands RMSF-root mean square deviation of indivi

[gmx-users] Protein Ligand simulation

Greetings to all ! i have completed Protein Ligand simulation as per the tutorial,my aim to proof that ligand A inhibit Ligand B -what are the possible analysis i can perform i have done the following RMSD - to see the stability of protein with ligands RMSF-root mean square deviation of indivi

Re: [gmx-users] protein ligand simulation

On Wed, Apr 20, 2016 at 10:27 AM, Justin Lemkul wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule >

Re: [gmx-users] Protein ligand simulation

On Wed, Apr 20, 2016 at 12:03 PM, Terry wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (terrence...@gmail.com) Add cleanup rule >

Re: [gmx-users] Protein ligand simulation

Hi, If you mean you can not see the group with command `gmx make_ndx -f xxx.gro`, that's because you have not created one for it. Consult the manual for how to use make_ndx. Terry On Wed, Apr 20, 2016 at 8:09 AM, bharat gupta wrote: > Dear Gmx users, > > I am performing a protein-ligand simul

Re: [gmx-users] protein ligand simulation

On 4/19/16 9:22 PM, bharat gupta wrote: On Wed, Apr 20, 2016 at 10:10 AM, Justin Lemkul wrote: On 4/19/16 9:08 PM, bharat gupta wrote: On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul wrote: On 4/19/16 9:01 PM, bharat gupta wrote: Thanks for your prompt response. On Wed, Apr 20, 2

Re: [gmx-users] protein ligand simulation

On Wed, Apr 20, 2016 at 10:10 AM, Justin Lemkul wrote: > > > On 4/19/16 9:08 PM, bharat gupta wrote: > >> On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul wrote: >> >> >>> >>> On 4/19/16 9:01 PM, bharat gupta wrote: >>> >>> Thanks for your prompt response. On Wed, Apr 20, 2016 at 9:31 A

Re: [gmx-users] protein ligand simulation

On 4/19/16 9:08 PM, bharat gupta wrote: On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul wrote: On 4/19/16 9:01 PM, bharat gupta wrote: Thanks for your prompt response. On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul wrote: [image: Boxbe] This message is

Re: [gmx-users] protein ligand simulation

On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul wrote: > > > On 4/19/16 9:01 PM, bharat gupta wrote: > >> Thanks for your prompt response. >> >> On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul wrote: >> >> [image: Boxbe] This message is eligible >>> for Automatic

Re: [gmx-users] protein ligand simulation

On 4/19/16 9:01 PM, bharat gupta wrote: Thanks for your prompt response. On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul wrote: [image: Boxbe] This message is eligible for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule

Re: [gmx-users] protein ligand simulation

Thanks for your prompt response. On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule >

Re: [gmx-users] protein ligand simulation

On 4/19/16 8:28 PM, bharat gupta wrote: Hi Justin, Here's the link for following files: complex.gro, CT3.itp (ligand topology), CT3.gro (ligand coordinates) and topology.top. https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA&usp=drive_web When I run make_ndx command using th

Re: [gmx-users] protein ligand simulation

Hi Justin, Here's the link for following files: complex.gro, CT3.itp (ligand topology), CT3.gro (ligand coordinates) and topology.top. https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA&usp=drive_web When I run make_ndx command using the solvated complex file (solv.gro), I don't

Re: [gmx-users] Protein ligand simulation

Dear Gmx users, I am performing a protein-ligand simulation using gromacs latest tutorial for 5.0.x version. As per the tutorial, I included the coordinates of the ligand in the complex.gro file (also updated total no. of atoms after adding ligand atoms) and updated the topology file (topol.top) b

Re: [gmx-users] protein ligand simulation

On 4/19/16 9:03 AM, bharat gupta wrote: Dear Gmx users, I am performing a protein-ligand simulation using gromacs latest tutorial for 5.0.x version. As per the tutorial, I included the coordinates of the ligand in the complex.gro file (also updated total no. of atoms after adding ligand atoms)

Re: [gmx-users] protein ligand simulation

Dear Gmx users, I am performing a protein-ligand simulation using gromacs latest tutorial for 5.0.x version. As per the tutorial, I included the coordinates of the ligand in the complex.gro file (also updated total no. of atoms after adding ligand atoms) and updated the topology file (topol.top) b

Re: [gmx-users] Protein - Ligand simulation

On 2/12/14, 3:35 AM, lucaam86 wrote: Thank you for your reply. Yes, I'm not specialist and I'm introducing now in Molecular Simulation. I don't know Steered Molecular Dynamic, do you have tutorials or guide documentations for it? Could you explain why the tutorial suggested by Aldo is not indic

Re: [gmx-users] Protein - Ligand simulation

Thank you for your reply. Yes, I'm not specialist and I'm introducing now in Molecular Simulation. I don't know Steered Molecular Dynamic, do you have tutorials or guide documentations for it? Could you explain why the tutorial suggested by Aldo is not indicated for me? Sorry for my lack of prepara

Re: [gmx-users] Protein - Ligand simulation

On 2/11/14, 2:48 PM, Aldo Segura wrote: You should take a look at this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html It's worth noting that while what the OP is trying to can be accomplished using SMD, the time investment would be quit

Re: [gmx-users] Protein - Ligand simulation

You should take a look at this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html Best, Aldo   === Aldo Segura-Cabrera Postdoctoral Fellow Division of Experimental Hematology and Cancer Biology Cancer and Blo

[gmx-users] Protein - Ligand simulation

Hi, I'm not a Biologist, I'm designer interested to molecular modelling and 3D visualization of proteins and molcules. I use gromacs but I'm not an expert of this. I would create an animation of the interaction between D-Alanyl -D Alanine carboxypeptidase and penicillin. In general i would see how