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Tagged with molecular-dynamics proteins
6 questions
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When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?
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 ...
5
votes
1
answer
658
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SARS-CoV - relative size of the spike protein
I am taking an online course in image analysis and have been asked to use the attached image to determine the size of the SARS-S protein of the SARS-CoV relative to the total of its proteins. However, ...
- 181
2
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Molecular dynamics simulation of a protein in acidic medium
I want to perform an MD simulation of a protein under acidic solvent conditions. A quick literature search seems to indicate that people are more interested in the protonation of protein side chains (...
- 455
3
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70
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Normal Mode Analysis of proteins
I'm trying to do Normal Mode Analysis for my MD trajectory. I'm following Amber tutorial (http://ambermd.org/tutorials/advanced/tutorial3/py_script/section5.htm) which uses an example of estrogen ...
- 229
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Molecular dynamics after modeling a protein loop. Necessary?
Firstly, I am postign this question to both chemistry and physics stacks exchange as I am not sure to which it belongs and to use the benefits from both sites.
I have modeled missing loops in a PDB ...
- 11
6
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How to write an entire trajectory into a single PDB file?
I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library.
With VMD if I do ...
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