Hey all. I am currently trying to use a molecular dynamics software (VMD or atomify) to explain the interaction between my aptamers and specific target to my audience. I have no idea were to begin, what parameters to feed into the software and how to generally go about this. This is actually my first time trying this. I will appreciate any help. or a referral to a helpful link as the videos on youtube haven't helped that much. Thanks in advance
I think this is way too broad of a question (and therefore answer) to be particularly useful. It's also not clear what you're asking.
to explain the interaction between my aptamers and specific target to my audience
Are you just looking for a visualisation/animation? or do you want to run proper analyses?
Molecular Dynamics is a huge field in and of itself, so you've got a lot of learning ahead to achieve even basic proficiency.
I'm no expert, though I've done some courses so perhaps the following very general pointers might help:
MD simulations are all about force fields (essentially the equations that govern the behaviour of the system). If you want to study effects in solution for instance, force field choice can be very important - especially since we don't have a completely perfect model of water. If I recall, AMBER is one of the most popular. I can't offer you any more information than this though really, it's often a case of optimising your set up, and/or picking a forcefield etc. with some kind of justification as to why).
You'll need 3D models (accurate ones) of all of your structures to feed in to the scenes you simulate. I believe Avogadro is very good for structure editing/building.
You probably don't need to delve 'fully' in to the world of MD to achieve interaction/docking simulations. From what I know of this area, AutoDock Vina is a very popular tool for docking studies, and has a comparatively low barrier to entry I think. It's usually intended for small molecule ligand - protein docking, but might work for your aptamers.
If you are just looking to visualise the docking/interactions or to create an animation and not actually do 'rigorous analysis', you might want to look in to Molecular Flipbook (for very rough approximations) or UCSF Chimera/PyMOL
I know it's been a while since this was posted, but just in case this is a helpful tool for a drug-protein binding-affinity prediction that takes in a SMILE sequence and an Amino Acid sequence and returns an integer that represents the binding-affinity. Here is the link to the model overview: https://model.modelforest.ai/binding-model