How to create Heme-CYS bond for CYP450 protein?

I would like to perform MD simulation study for CYP450 proteins in gromacs 4.6.7 with gromos53a6.ff. When I prepare the system for simulation, i have got error that gb_, ga_ and gd_ were not found...

03 April 2016 9,018 3 View

How can one transfer all ligands from templates to final homology model?

I have 3 X-ray structures with co-crystallized ligand in active site. How should I actively copy all ligand in this same position from all temple to the final homology models? I perform homology...

01 February 2015 916 3 View

Can anyone help with molecular dynamics and protein equilibration?

How should I perform correct equilibration of my protein before I run molecular dynamics.

06 July 2014 1,307 6 View

Which of the CHARMM force field versions is better for protein structural biology studies?

Charmm27 or Charmm36?

04 May 2014 4,762 2 View

What kind of analyses should I use to determine the affinity of peptide-protein interaction after molecular dynamics?

I have done a 50 ns molecular dynamics symulatuion for protein-peptyde complex in NAMD, and now I want to calculate strenght of the protein-peptide interaction. What is the best way or ways to the...

03 April 2014 7,389 4 View

Can anyone help with modeling protein disorder region?

I have to predict 3D structure of protein with long (70 a.a) N-terminal disorder region. Is there any best method for predicting the fold for this disorder region, or only way is use molecular...

02 March 2014 5,970 5 View

Is there a good way to prepare molecular dynamics simulations?

Is there a good way to add crystallographic water to structure used, for example, dowser software, while preparing protein structures for molecular dynamics simulations?

02 March 2014 2,346 8 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 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

MD MOE RMSD

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

07 August 2021 0 0 View

MGL tools

20 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

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 climate change will influences human and animal behavioral change?

The role of climate change influencing the human behavior as well as economics interest

01 June 2021 0 0 View