05 May 2014 1 1K Report

See above

More Udhaya Kumar's questions See All
Is there a Gromacs Tutorial to add a residues to a force field and modifying a .rtp, .itp, atomtypes.atp and residuetypes.dat file?

If anyone have gromacs tutorial to a new residue to the topology. The protein which I am working on has 4 NAG (N-acetyl Glucosamine) and 1 ALS (2-amino 3-oxopropionic acid). These residues were...

05 June 2015 2,207 3 View

Why do I get huge fluctuations in RMSD when I simulate a protein in 20ns using Amber99sb force field in Gromacs 5.0.4?

I have followed the "Tutorial for Trypsin-­‐Benzamidine complex molecular dynamicsstudy" (pdf file attached below) and some of the inputs i have changed according to my protein name and ligand...

02 March 2015 6,121 7 View

How to include the residues N-acetyl Glucosamine (NAG) and 2-amino 3-oxopropionic acid (ALS) in gromacs 4.6.5 version's topology ?

My protein has 4 NAG and 1 ALS residue in its sequence. When I tried to simulate the protein using gromos96 53 a6 force field , it's showing a fatal error as: residue 'ALS' not found in residue...

31 December 2014 6,092 4 View

How to install Tinker (Molecular design software) in ubuntu 14.04 version ?

TINKER is a molecular modelling software, the user guide is difficult to understand and install the software.  Have any of you installed it before ? I need the detailed steps for installation. Any...

11 December 2014 6,319 3 View

Can anyone tell how to install gromacs on Ubuntu 14.04 ?

I am using ubuntu 14.04 version, please tell me which version of GROMACS I have to use for this ubuntu 14.04 version. And give me the Installation steps. I have installed cmake and c++98 compiler.

11 December 2014 7,278 4 View

Similar questions and discussions
Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 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

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 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

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 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

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...

28 July 2024 2,136 4 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View

Our partners will collect data and use cookies for ad personalization and measurement. Learn how we and our ad partner Google, collect and use data. Agree & close