Fossil Cladocerans? Dear Colleagues! My team is very interesting t look at them (at least images)...Do you have any fossil cladocerans to study?

Any references about insects or animals that can damage or weathering of rock or fossil material?

Are there any references to insects or animals that can cause damage or weathering to the rock or fossil material? books or paper that would be nice. Thank you very much!

24 February 2021 6,805 3 View

Does AMBER or CHARMM force field parameters have coarsed grained side chain parameters?

I need to coarse grain the side chain with a single atom. However, what force field parameters do I have to use. Does AMBER or CHARMM have any parameters and partial charges for coarse-grained...

31 January 2021 7,091 3 View

The lipid bilayer broken down and form micelle within 1ns MD simulation. How to simulate lipid bilayer without breaking bilayer?

To simulate the lipid bilayer (10-10, 25-25 so on) from CHARMM-GUI membrane builder, we used to simulate it at various force field (AMBER14, AMBER03, AMBER14IPQ, AMBER15FB, NOVA, YAMBER) at water...

26 January 2021 7,816 2 View

AMBER tleap solvatebox always undervalues the density, why?

I've been searching for an answer to this question for years, and I'm shocked I haven't found any discussion on any forums. Here is an example to provide more details: I am preparing a 450...

20 January 2021 7,561 2 View

What species (or genus even) of crab is this (bivalve using hermit type)?

Two weeks ago I found a peculiar crab in the intertidal zone in SW Florida. when found, the crab was not utilizing a shell. It was similar shaped to porcelain crabs found in our area, but with...

17 January 2021 1,620 4 View

Can i use MM-PBSA to calculate the binding energy of a glycan ligand? ad how?

I have a protein-ligand (glycan) complex and want to do an MM-PBSA analysis using AMBERTOOLS after doing MDS (NAMD). What are the files necessary I should prepare for glycan? Note: I used...

30 December 2020 2,658 2 View

Is there anyone who can help me parameterizing theligand molecule with AMOEBA polarizing force field for using it in AMBER?

I am able to generate the parameter topology files for protein and water box using TINKER but am not able to generate these for my ligand as it is finding no atom types and atom class in TINKER....

17 December 2020 4,309 1 View

Any Molecular Dynamics Tutorial for Membrane-Bound Proteins in Amber?

Hi everyone I'm currently working with a membrane transporter protein to which I need to simulate molecular dynamics (MD). For this, I have inserted my protein in a membrane with CHARMM-GUI and...

16 December 2020 407 1 View

Since I am design automatized grader for forest seeds, it is important for me to know the following?

1. Is there a difference between a dormant seed, for example, of Scots pine, a fossilized dead seed, and an active live one by spectrometric or other characteristics? 2. Is it possible to...

26 November 2020 9,275 2 View

Which are the drawbacks of using a medical CT for scanning fossils?

I am in the need of scanning some fossils for analyzing their inner structure. Unfortunately I don't have access to a proper CT or micro-CT of industrial use that suits nicely fossils and neither...

16 November 2020 1,748 6 View