GROMACS version: 2019
GROMACS modification: No
Hi All,
I am going to do MD simulations on a cross-linked polymer. I want to use amber force field and gromacs 2019. However, for the preparation of input file, I want to use ambertools. I read the follwing tutorial for that,
https://ambermd.org/tutorials/advanced/tutorial27/pet.htm
but my polymer has cross link and I don’t know how can I define the cross link by LEAP module in ambertools. Its highly appreciated if you can help me.
Best,
Questions about using AMBER should be posted to their mailing list.
Sorry for my mistake. I there any way to prepare the input files of cross-linked polymer in gromacs? As I want to do the MD by gromacs.
Best,
I think that you should prepare your initial conformation as a model structure, manually. Then, prepare your force field parameters.
To prepare gromacs parameters of amber type of force field you can use the combinations of ambertools (tleap) with ParmEd.
Another force field choise is charmm force field (22 or 36). If you want to prepare charmm22, you can use swissparam. In case charmm36, you should use cgenff.
I do not exactly know which one is a suitable way for your system.
Good luck.
Thank you for your reply. Could you explain the tleap usage in details? I want to employ amber force field. Finally I will convert output files to gromacs.
Best,
I am sorry for that it is GROMACS forum. It should be discussed in AMBER mailing list.
Polymer cross-links are introduced via specbond.dat in GROMACS when running gmx pdb2gmx See http://manual.gromacs.org/documentation/current/reference-manual/topologies/pdb2gmx-input-files.html#special-bonds