Question: Molecular dynamics simulation of ssDNA with targets in solution, How do I achieve this?
gravatar for jaqx008
2.8 years ago by
jaqx00870 wrote:

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

ADD COMMENTlink modified 6 weeks ago by casey20 • written 2.8 years ago by jaqx00870
gravatar for Joe
2.8 years ago by
United Kingdom
Joe18k wrote:

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:

Force Fields

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).

Building Models

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

ADD COMMENTlink written 2.8 years ago by Joe18k

Thank you so much Healey for your response. I do not want to go too deep and just need visualization to show the interaction between my aptamers and the target molecules. Im not sure I want to go deep into all the math. I will see if I can make 3D of all my molecules and try one of the tools you provided. Its just an idea I am trying to build on and I feel for my up coming presentation, the audience would appreciate something like that. Thank you

ADD REPLYlink written 2.8 years ago by jaqx00870

I would start off with something like UCSF Chimera in that case. It has plugins for MD and Docking studies, whilst also being a 'self-contained' and fairly user-friendly package.

At the absolute simplest level, you can manipulate molecule models individually, so you could position them by hand if you just wanted to give your audience an idea without actually worrying about the 'science' too much.

ADD REPLYlink written 2.8 years ago by Joe18k

Yes. This sounds exactly right. Thanks for understanding what Im trying to do. I will get back you on the results I get.

ADD REPLYlink written 2.8 years ago by jaqx00870

Thanks. I was able to get something to include in my slides and it really helped. I am now looking to try different studies on binding energies etc, I need this so that when i try to publish, I won't have much worries. Once again, Thanks

ADD REPLYlink written 2.8 years ago by jaqx00870

Ok, great. Remember to accept the answer if it solved your problem so that the thread doesn't stay marked as unanswered for others.

ADD REPLYlink written 2.8 years ago by Joe18k
gravatar for casey
6 weeks ago by
casey20 wrote:

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:

ADD COMMENTlink written 6 weeks ago by casey20
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