Re: [gmx-users] Fix the residues

Is TYR and SER are N-terminal and C-terminal residues , respectively? Also, you may compare the corresponding atoms of each residues with same residues present in your system and does not show the mentioned warning. All the best On Fri, Jan 6, 2017 at 10:58 AM, liming_52

[gmx-users] Regarding calculation of diffusion constant (through MSD) of solvent molecules near protein surface

Dear All, Say I want to calculate how the water molecules near the surface of protein are diffusing, how would I do that? Say I look at some hydrogen bonding interactions using VMD and zoom in and identify the SOL molecules around the surface . Can I create an index file containing those

Re: [gmx-users] Topology parameters for ligand

I got it. I have looked at the input files for the T4-lysozyme tutorial available at alchemistry.org. They have defined state A and state B. I am using GROMACS-5.1.4 for these calculation. So as mentioned in gromacs manual decoupling parameters are taken from the mdp options, like by defining

[gmx-users] Mycobacterium cell wall protein

Dear Gromacs Users, I have a insilico model of Mycobacterium tuberculosis cell wall (surface) protein which has no transmembrane helices. Which Gromacs tutorials should I follow for MD studies to know about its conformational stability and latter for protein - ligand studies. Kindly guide me

[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] Free energy calculation of protein and drug

Hello Tasneem, Same like you, I'm pretty new to this field too. I don't know enough how to calculate free energy in gromacs. I did only MM/PBSA for binding energy calculations. I'll let you know if i get some thing relevant to your question. All the best. Thanks On Thu, Jan 5, 2017 at 10:28

Re: [gmx-users] pulling protein-ligand complex

Sincere apologies... I have uploaded the files here... https://drive.google.com/drive/folders/0B6O-L5Y7BiGJT29hSGlEWTM3Zk0?usp=sharing I'm running another pull experiment with "pull_rate1 =0.01". On Sun, Jan 8, 2017 at 10:23 PM, Justin Lemkul wrote: > > > On 1/8/17 1:52 AM,

Re: [gmx-users] pulling protein-ligand complex

On 1/8/17 1:52 AM, abhisek Mondal wrote: Alright. I'm attaching md_pull.mdp and sumary_distances.dat file. May be I have set pulling rate very low. Anyway have a look. The list does not accept attachments (if I had a nickel for every time I said this...) so upload the files somewhere and

Re: [gmx-users] Regarding gromacs commands..

On 1/7/17 10:58 PM, Dilip H N wrote: can i create it with Avogadro molecular editor software..?? Probably, but that's a question for whatever help forum they provide. I tried creating using this software,, than if i compile it and run the command of mdrun.. it is giving segmentation

Re: [gmx-users] Topology parameters for ligand

On 1/7/17 10:29 PM, tasneem kausar wrote: Thank you for your reply In last section of your tutorial you have suggested some changes to made in mdp file. That can be used for solvation free energies. For free energy calculation of protein drug complex, is it only lambda restraint to be

Re: [gmx-users] LJ Interaction between 2 groups looks unusual

Hi, We can't see your figure, but as you would see in the mdrun log file, energy groups are not implemented for gpu runs. You can do mdrun -nb cpu -rerun however Mark On Sun, 8 Jan 2017 07:23 Mijiddorj Batsaikhan wrote: > Dear gmx users, > > I run 500 ns simulation