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

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

Problem of using NAMD?

05 June 2016 1,484 0 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

What is your perception on using visual analysis or quantitative approaches to evaluate data from single-case research designs (n of 1 trials)?

Results of single-case research designs (i.e., n-of-1 trials) are often evaluated by visually inspecting the time-series graph and computing quantitative indices. A question our research team is...

03 March 2021 687 1 View

How to calculate BREQ 3 questionnaire?

how to calculate BEHAVIOURAL REGULATION IN EXERCISE QUESTIONNAIRE BREQ 3 ,which contain 24 questions and each question has 5 answers (0- Strongly disagree , 1-disagree, 2- Neither agree nor...

02 March 2021 811 3 View

I am interested in medicinal chemistry field, which books are highly recommended to learn from?

I am at the beginner level in drug design and drug discovery, and I am interested to learn more about this field. Which books are highly recommended to start from and gives me all essential...

02 March 2021 8,437 2 View

Please suggest a good text book for "Research Methodology in Life Sciences". Which book would be good for PhD Scholars?

Please provide Book Title and author name

02 March 2021 9,059 3 View

Could any one guide me, to write research proposal for grant? ?

We have one plant, the local people using this for controlling blood sugar, the toxicity and antidiabetic activity of the plant is not reported yet, please guide from whag should be the process ?...

02 March 2021 2,300 1 View

Which is suitable for use with Python? MySQL or SQL Server?

Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?

01 March 2021 3,422 3 View

How to address this issue in the analysis of Real-Time PCR results?

To dear Researchers, I was analyzing a series of concentration for estimation of Real-Time PCR efficiency. The concentration was 1:10. I used MS-excel to evaluate Slope. The result of slope was -8...

01 March 2021 8,683 4 View

Can Virtual Servers (remote dekstop manager) run heavy ANSYS Fluent CFD simulation ?

I have a virtual machine. My host Pc specs are not that good thats why i went for virtual servers. so basically my host pc has 8gb of ram with nvidia quadro k2200 4Gb DDR5 GPU ,processor intel...

01 March 2021 8,415 1 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View

Is anyone familiar with the cyclic compressive fatigue testing (BS EN 12697 - 25) ?

I would like to get more information on the cyclic compressive fatigue testing (BS EN 12697 - 25) which is typically done for bituminous material in pavement design. Any one can advise on the...

28 February 2021 2,004 3 View