Questions tagged [proteins]

Question 1

Do I need to edit position restrain file for both protein and ligand manually, or may I perform changing parameter "define" from NVT.mdp and NPT.mdp files? Total number of atoms before ...

Question 2

I want to compute the binding free energies of water molecules around proteins, and I want to know if there is information comparing the accuracy of MD/GIST based methods such as WatSite, WaterKit, ...

Question 3

I am researching the areas of protein structure prediction, protein + ligand pose prediction, and co-folding algos with deep learning. I am trying to map the current state of the art architectures ...

Question 4

I have a very small part of a protein that is supposed to be helical. However, in molecular dynamics simulation, it unfolds and gets into extended conformation. Is there any way I can force it to stay ...

Question 5

I used Autodock Vina and UCSF Chimera to perform blind and targeted docking on a protein from the RCSB database and a molecule I had optimized with Gaussian software.The results are as follows: The ...

Question 6

I started optimising a system containing amino acid residue, water molecule and a toxic metal ion, in proving a supposed reaction steps that might take place in inhibiting enzyme activity. The ...

Question 7

Suppose I designed a novel coarse-grained model of polymer chains. How can I test the validity of my novel model? Is there any applied framework available?

Question 8

Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled ...

Question 9

So far i have found only one paper that describes how we can compute protein energy while doing MD simulation: Nishikawa, Ken, Motohisa Oobatake, and Tatsuo Ooi. "Method for Energy Computation ...

Question 10

I see that some free MD simulation software are available online. VMD NAMD LAMMPS OpenMM GROMACS Amber CHARMM Which one above is the most appropriate for protein simulation?

Question 11

Suppose I have a protein PDB file, and I want to know which atoms have bonds between them. How can this be done? Sometimes people suggest using the CONECT field for ...

Question 12

I'm interested in bound ions in protein xray crystal structures. Of course a lot of structures include biologically significant ions, such as Mg2+ in the active site of an enzyme. But a lot of ...

Question 13

In optimising proteins with DFT/B3LYP, how can we detect the charge and multiplicity of the protein?

Question 14

I am very new to Pymol and was trying to figure out how I can find the largest distance between 2 residues. Using just the basic distance function I get multiple distances which is not very useful in ...

Question 15

Suppose, I want to develop a novel force field for proteins. What is the empirical procedure I should follow to do that?

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Questions tagged [proteins]

Performing two (restrained and unrestrained) NVT and two (restrained and unrestrained) NPT ensemble for 200ps in a protein-ligand complex

Comparison of GIST-based water scoring tools - WatSite, WaterKit, AutoDock-GIST

Protein structure prediction: levels of coarse-graining in deep learning approaches

Restrain a protein to be helical in an MD simulation

Blind docking and targeted docking

Why is this geometry optimization in Gaussian not working for a system containing an amino acid, a water molecule and a metal (Pb) ion?

How do I validate and benchmark a new protein or polymer model?

When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?

Method for Energy Computation of Protein Structures

Which MD software is preferable for protein simulation?

From a PDB file, how may I know which atoms have bonds between them?

How easy is it to distinguish water from ions in xray crystallography?

How to select charge and multiplicity for macro-molecules?

How to find the smallest distance between 2 residues in Pymol?

What is the procedure to develop a new force field for molecular simulation?

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