How can I split a Gromacs .tpr file?

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Can anyone tell me how i can reterive complete bacterial data from KEGG?

I Want to download complete KEGG bacterial data please guide me how i can do that? or if any one have this data kindly send me. its not freely available for academic user too.

06 July 2019 9,038 6 View

Does PME requires periodic boundry condition using extend or restart file in namd?

Hi, I have a protein complex system, Initially i have minimized and equilibrate my system for 0.5ns. Then i want to slowly relax the side chain and back bone of my protein. i used all the restart...

09 October 2016 7,585 3 View

What is meant by Umbrella sampling and why it is require for PMF calculation in MD Simulation?

Hello, I want to know about umbrella sampling, and why it is required for potential of mean force for MD simulation?

08 September 2016 3,333 2 View

Which tools can plot inter-hydrogen bond interactions graph?

i want to plot total number of inter-molecular H_bond interactions between the drug compounds and target protein like below mentioned...

07 August 2015 4,294 13 View

Why Gromacs 4.5.6 does not generate .xtc file?

Hello, I am using Gromacs 4.5.6 version for protein ligand MD simulation. i completly follow Bevan La...

06 July 2015 6,825 9 View

How to convert amber topology and cordinates files into gromacs topology and cordiante file?

Hello, I want to run protein ligand MD simulation using Amber99sb force field. i generated protein topology files using gromacs easily but when i generated ligand topology using AmberTools15 and...

05 June 2015 5,096 3 View

How do I calculate binding free energy of simulated antigen-antibody structure?

I want to calculate binding free energy of antigen-antibody complex after 30ns MD simulation. I used MMPBSA but it takes approx 12 days for 1 ns (500 frames) of antigen-antibody complex in which i...

01 February 2015 3,152 15 View

Which is the best computational software to remodel antigen-antibody?

I downloaded PDB ID 4I3S it contains 16 missing residues in heavy chain of antibody as well as in antigen. I want to remodelled it before running the simulation. Which is the best computational...

10 November 2014 5,339 10 View

How can I calculate the half life of an inter-hydrogen bond?

I want to calculate the half life of inter hydrogen bond of antigen and antibody. How I can do this?

06 July 2014 1,226 0 View

How can I calculate inter-hydrogen bonding between an antibody and antigen using pymol?

i want to calculate inter-hydrogen bonding between antigen and antibody using pymol. how i can calculate it and how i can get the hydrogen bonding log file?is there any way to get pymol log file...

05 June 2014 7,099 3 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,989 3 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View

Transfection in HEK293T cells?

Dear All, I am trying to transfect a pCDNA3.1 vector containing my gene of interest. The purpose is to figure out the localization of the protein of interest. I have fused the protein with GFP on...

31 July 2024 9,892 4 View

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

31 July 2024 781 1 View

How to retain the a GFP tagged gene expression in stable cell line?

Hello , I established a stable cell line expressing GFP tagged to a centrosomal gene having G418 drug selection marker. I validated the stable line by IFA and Western blotting, results are fine....

29 July 2024 5,007 0 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

What is the relationship between protein structure and N or C terminal tagging choosing?

I want to do 2,3-butanediol dehydrogenase(BDH) enzyme purification to confirm its activity for 2,3-butanediol. Before that, I need to confirm which N or C terminal tagging is better for enzyme...

28 July 2024 366 3 View

Why cannot i find my protein on cell surface after antibiotic selection of expressing plasmid?

I cannot confirm cell surface protein expression by flow cytometry even after transfection and antibiotic selection of cells. Does it take long for proteins to express on the cell surface? the...

28 July 2024 3,178 3 View