Why do we need molecular dynamic simulation of protein-ligand complex? what is the important
I want to perform MD simulation of protein-ligand complex using VMD-NAMD. When I want to create protein structure file (PSF), there is dialogue box asking me to parameterize my ligand.
08 September 2016 4,988 5 View
I want to perform simulation and when I run the command prompt window with the following syntax " namd2 ubq_ws_eq.conf > ubq_ws_eq.log &" below error will appear" Charm++ fatal error:FATAL...
06 July 2016 1,238 19 View
I have tried several times to access this server (http://www.ddg-pharmfac.net/vaxijen/), but I could not. Can anyone help me with appropriate link to this server
06 July 2016 8,765 2 View
I want to build a model of query sequence (qseq) based on the alignment against the multiple templates using the `model_mult.py'. from modeller import *from modeller.automodel import * env =...
05 June 2016 5,309 4 View
I have problem in running NAMD, it usually display fatal error message " No simulation config file specified on command line" despite the fact that I have installed the mpi_x64.msi.
05 June 2016 1,654 0 View
I have a protein sequence but I checked PDB for the purpose comparative modeling, but I couldn't find any similar protein with known 3D structure, yet I want model my protein. Beside ITASSER which...
04 May 2016 7,622 4 View
BIOINFORMATICS
04 May 2016 614 4 View
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
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
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
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
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? For example consider a process for certain product manufacture where a new process flow...
31 July 2024 781 1 View
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
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
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
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