Mustafa Alhaji Isa

8 Questions 33 Answers 0 Followers

Questions related from Mustafa Alhaji Isa

How to parameterize ligand in MD simulation using VMD-NAMD?

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.

09 September 2016 4,945 5 View

Problem of using command prompt window in molecular dynamic simulation?

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...

07 July 2016 1,176 19 View

Problem of accessing VaxiJen - Drug Design Group server?

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

07 July 2016 8,729 2 View

Problem of using NAMD?

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.

06 June 2016 1,615 0 View

How do I generate DOPE score using multiple template (model_mult.py) in modeller 9.16?

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 =...

06 June 2016 5,276 4 View

Please can someone tell me which software should I use to determine the 3D structure of protein without any similar sequence in PDB?

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...

05 May 2016 7,595 4 View

How do I refine my 3D model using modeller to minimize energy?

BIOINFORMATICS

05 May 2016 574 4 View

Why do we need molecular dynamic simulation of protein-ligand complex?

Why do we need molecular dynamic simulation of protein-ligand complex? what is the important

05 May 2016 3,624 0 View