When I tried to follw the tutorial and add the ions. This error showed up. I will also upload the file dxc_fix_AC.prmtop (I have changed the extension to .mdp so that I can upload the file)
dxc_fix_AC (copy).mdp (43.2 KB)
I have prepared the ligand parameters and topology using the acpype (Amber).
Please provide some helpful suggestions.
The attached file AMBER-formatted topology file. You can’t use it with GROMACS without converting it to an appropriate format.
Dr. @jalemkul thank you for the information. Before moving on to Amber, I am first trying to use the charmm force filed (following your tutorial but with my protein and ligand) and wanted to see how its different from AMBER force field result.
One more question, I am still confused regarding on what basis you decide what forcefield to consider?
Thank you.
Use the best tool for the job. Have previous investigations established validity of the force field in similar systems? Does the force field cover everything I need, and if not, is it straightforward to parametrize something new given available literature information and tools? Some of this really comes down to personal preference and what you’ve been trained in using.
Thank you Dr. Lemkul. You have a been a constant source of information and useful suggestions. I am reading more literature to understand the world of Molecular Dynamics Simulations. I am following your suggestion, “trying to walk first before running” :)
But how? How can I convert to prmtop to gromacs field? why we don’t have ability to apply everything is same place. I mean why can I create ligand forcefiled in gromacs. In two says, I am trying to concert but I am failed. please help me. I have the same problem and I started using Gromacs this week.
when I convert the parameters which I created in amber
Which gromacs extension should I write here?
http://www.mdtutorials.com/gmx/complex/02_topology.html
Please guys, these are really old stuff, lots of confusion, and I don’t know why google does not get you to the right place if searching for acpype:
Start from here:
Make sure to read the instructions carefully. Most importantly, learn about the tools limitations, look into some of the tutorials in the Wiki Home · alanwilter/acpype Wiki · GitHub and read the FAQ as well.
I know it takes time to learn these new things but it takes even more (muuuuuuuch more) time to develop it. So, a day or so reading about it and trying really worth your (and our) time before coming to ask for help.
thank you!! I have the same question about google
