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

Problem of using NAMD?

05 June 2016 1,484 0 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

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

What is the most Operating System (OS) which can be INSTALL on Tiny hard devices like Raspberry Pi (RPi) hardware ?

I'm targeting to deploy a mesh network and manually configure MANET routing protocols. I'm preparing scenarios, architectures, and hard devices needed to do that. Are there some step-by-step...

03 March 2021 1,931 5 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

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View