How can I convert a trajectory file from GROMACS (trr or xtc format) to AMBER (ASCII or NetCDF format)?

How can I convert a trajectory file from GROMACS (trr or xtc format) to AMBER (ASCII or NetCDF format)? I have always seen tutorial about the revers procedure, ie from AMBER to GROMACS...

06 July 2014 2,025 4 View

Can you help me with alanine scanning with AMBER?

From what I have understood (from the AMBER manual) I have to prepare the topology of every single mutant I want to scan and, subsequently, I have to start an individual run (with the MMPBSA.py...

05 June 2014 3,513 1 View

Can anyone help with a forcefield with halogen bonding treatments?

I am looking for a forcefield in GROMACS which better characterizes the TCDD ligand. In particular I have found that OPLS-AAx seems suitable [J Chem Theory Comput. 2012 Oct...

01 February 2014 4,920 4 View

Do you know of any similar tool like MMPBSA.py for GROMACS?

Since I have MDs produced with GROMACS, are there available any tool for calculating dGs with MM/GBSA method? (and, in the meanwhile, without converting trajectories in AMBER format?)

01 February 2014 7,109 9 View

Description of OPLSaa forcefield?

Does anyone have a "reference manual" of such forcefield? (especially the related top files in GROMACS) e.g. what are the atom types included and what they describe, etc. etc.

31 December 2013 5,485 3 View

Do you know of any similar tool to OPLS-AA for making topology file?

I need to create a topology file (.top for GROMACS) of 2,3,7,8-TCDD (dioxin). In particular my topology file will have to be suited for implementing OPLS-AA forcefield, since I know that the...

31 December 2013 1,871 9 View

How to graft short oligopeptidic linkers to substitute long loops?

I have to accomplish an homology modeling task in which the reference template does not cover very large loops of the query sequence (20-30 residues). I have not found any reliable alternative...

11 December 2013 8,405 3 View

Tutto molto interessante

01 January 1970 1,029 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

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