Does anyone know why am I getting the error using HADDOCK 2.2 web server?

I am trying to dock two proteins using HADDOCK web server (prediction interface). I have done the changes reres, delocc... but I still having the error message: First pdb file contains multiple...

01 February 2017 2,971 3 View

Is possible to simulate a trimer using gromacs package?

10 November 2014 9,318 6 View

Can anyone help with FEL (Free energy landscape)?

I have computed a representation of the free energy landscape (FEL) sampled by my trajectories of MD following the tutorial as attaching . I would like to know if there is one specific reason as...

06 July 2014 5,827 2 View

How do you represent the three subunits of a trimer using VMD, PyMOL or Chimera?

I have a protein pdb file (only one subunit), but I want to represent it in the form of a trimer (as attached).

06 July 2014 3,249 3 View

Can anyone help with using -fit rot+trans?

I tried to fit the whole trajectory from molecular dynamics simulation (using Gromacs) using the initial structure (using -fit rot + trans), but when I compare two structures they are not aligned....

05 June 2014 6,564 8 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 analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 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

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 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