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

08 September 2016 4,857 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...

06 July 2016 1,105 19 View

Problem of accessing VaxiJen - Drug Design Group server?

06 July 2016 8,662 2 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 =...

05 June 2016 5,206 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...

04 May 2016 7,528 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

04 May 2016 3,531 0 View

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

BIOINFORMATICS

04 May 2016 485 4 View

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 View

Can we classify HV and LV lines based on line length?

I have dataset which shows the length of power lines. I need to classify the lines based on the line length. Is there a rule to classify the High voltage (HV) and low voltage (LV) lines based on...

03 March 2021 4,116 4 View

I got 02 moderator values defining Johnson-Neyman significance regions. Is it an error?

Hi everyone, I am conducting research for my Master's thesis. I am using PROCESS by Johnson-Neyman to analyze my Moderator model. I test the relationship between Public Service Motivation and...

03 March 2021 2,350 2 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

Do I need to strip the PVDF membrane before staining it with colloidal gold?

Dear Colleagues, After running Western blot on PVDF membrane and detection using ECL, I would like to stain my PVDF with colloidal gold to be able to allign the ECL image with total proteins on...

02 March 2021 7,829 3 View

PACYC PCR not working after several attempts. Would anyone have any suggestions?

So, I have been trying to run a pACYC PCR which will be used later on for a Gibson Assembly. However the PCR is not working. I have already tried gradient PCR and changing extension time; however...

02 March 2021 1,146 2 View

What SPSS analysis should I run with one IV (with two levels) and two DVs?

Hi, I am trying to figure out which test would be most appropriate to run for the following question: Is there a difference in task blood pressure between smokers and non-smokers? There are two...

01 March 2021 8,235 2 View

How can I integrate a routing protocol in a tiny device (e.g. Raspberry Pi)?

Hi Community, I'm facing the issue of integration/compiling a new routing protocol in a WSN simulator. The final goal is to successfully add, configure this routing protocol in hardware devices...

01 March 2021 9,332 6 View

OpenBCI eeg--has anyone used them?

I'm looking to try out an off-the-shelf EEG set for some exploratory work. Curious if anyone has used the OpenBCI, and how much set-up work is required. I've heard they are more difficult to get...

01 March 2021 4,128 3 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View