How to build the topology files for Broken DNA?

hello, I want to do gromacs simulation of a protein DNA complex along with a small molecule ligand. But unfortunately the bound ligand is not a complete one..its one helix is cut. So, i am...

11 December 2018 3,742 6 View

Why one chain break are connected during the energy minimization?

We have placed a dimer protein into gromacs energy minimization utilising OPLS force fields. but after running 9567 its get minimized. But the problem is that after energy minimization one gap...

11 December 2018 8,799 4 View

Fatal error: Syntax error - File ligand.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes?

I want to perform a protein-DNA-ligand complex simulation by gromacs. but my system contain two ligands named PTR and LIG. but when ever i am going to perform the energy minimization. This is...

11 December 2018 4,118 2 View

Protein Homology modelling?

I have a trimeric protein which have a lots of missing residues. that why i decided to build homology modelling. but after successfully modelling each chain contains maximum loop like structure...

03 April 2018 8,272 5 View

What is the reason for increasing RMSD?

I have a protein containg 2138 amino acids in each chains. then i added POPC membrane and then add solvent ater and counter kcl ions..then i had done 025ns run for eqilibration by restrating...

08 September 2017 3,045 5 View

Protein-Ligand-DNA simulation

Hello Everyone, I have a AUTODOCK docking PDB file for both Protein-Ligand-DNA Complex. I want to do simulation of these complex. but simulation failed due to unrecognized ATOM TYPES present into...

05 June 2017 5,315 5 View

Protein-ligand simulation in Gromacs

05 June 2017 7,607 15 View

ACPYPE error

I asked you a question about some problems regarding the ACPYPE error. I installed the ACPYPE according the https://code.google.com/archive/p/acpype/wikis/TutorialAcpype4Gromacs.wiki.but when I...

05 June 2017 6,462 0 View

Steered Molecular Dynamics?

11 December 2016 4,458 1 View

Why TLR7 specific antagonist is not found right now?

we didn't find any specific TLR7 specific antagonist . maximum are dual antagonist of TLR7 and TLR9 antagonist. Is there any specificity on the protein active site? what was the reason for that?

08 September 2016 8,478 6 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

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

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 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