Is it possible to take a pdb file generated from docking results for molecular dynamics study in VMD and NAMD system?

I want to use a pdb file got after docking of a ligand to protein using autodock4 in molecular dynamics calculations with the help of VMD and NAMD only. I have a very little idea about VMD as well...

08 September 2018 7,894 0 View

How can I calculate polarizability and hyperpolarizability using Gaussian? What are keywords for it?

I was tried the keyword "polar" for the calculation. I was unable to get the result. I need a suggestion about it. Please tell me keywords that I can use it in Gauss view 5.0 for calculation....

07 August 2015 1,261 7 View

Can anybody help me about DOCKING of DNA by autodock4?

31 December 2014 7,947 4 View

Uploading problem: how can I upload structure factor file?

09 October 2014 7,564 0 View

How can I get supplimentary file of a crystal after solving X-ray crystal data?

Method to get supplimentary data using Appex and WinGX software or any other sources?

31 December 2013 8,338 3 View

How can I install gromacs-3.3.1 on windows?

I have no idea about compiler. Please help me.

01 January 1970 4,892 0 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

Why does blocking with my immunogenic peptide cause nuclear fluorescence in ICC?

Hi all, I am validating a polyclonal antibody raised against human ANT4, through WB and ICC. In most of my controls, the antibody shows very little off-target binding, but when I pre-incubate the...

03 March 2021 5,999 3 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View