Hi users,
I found the topology files for choline with GAFF ff in literature (coa.ff and colinab3lyp08.prepi.txt) and I would like to convert these file to the input files I can use in Gromacs. I knew that with Amber you can convert these sort of files to top file and crd file in Amber and then convert these files to top file and gro file in Gromacs. I don't have access to Amber (it's not free) so I wonder if there are other ways to help me getting there. I tried to convert these files manually, but the atom types in Amber for GAFF are not the same with those in Gromacs for GAFF. Maybe I am missing something here? Please correct me if I'm wrong. Thanks in advance!
Reference: Article Interaction and dynamics of ionic liquids based on choline a...
Hi Peiyin! You can use for that acpype.py together with antechamber. Then you will get input files for gromacs which will be compatible for running calculations with AMBER FF. All what you need is pdb and mol2-files. There you shall name atoms for your molecules so that you won't get names which might be "unconfortable" to use.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
Please look into this. This will be useful for topology conversion.
As Amber Antechamber uses the GAFF ff, a script known as ACPYPE, which is a Python interface for Antechamber can be used to write GROMACS topologies. It can be found here in this link.
http://code.google.com/p/acpype/
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