# Cross linking of polymer **URL:** \ **Category:** User discussions\ **Created:** [July 7, 2020, 6:00pm UTC](https://gromacs.bioexcel.eu/t/cross-linking-of-polymer/437 "2020-07-07T18:00:09Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![sako132002](https://avatars.discourse-cdn.com/v4/letter/s/a9adbd/32.png) [@sako132002](https://gromacs.bioexcel.eu/u/sako132002)\ **Post date:** [July 7, 2020, 6:00pm UTC](https://gromacs.bioexcel.eu/t/cross-linking-of-polymer/437/1 "2020-07-07T18:00:09Z")
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](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, ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [July 7, 2020, 6:12pm UTC](https://gromacs.bioexcel.eu/t/cross-linking-of-polymer/437/2 "2020-07-07T18:12:36Z")
Questions about using AMBER should be posted to their mailing list. ---
**Author:** ![sako132002](https://avatars.discourse-cdn.com/v4/letter/s/a9adbd/32.png) [@sako132002](https://gromacs.bioexcel.eu/u/sako132002)\ **Post date:** [July 7, 2020, 6:52pm UTC](https://gromacs.bioexcel.eu/t/cross-linking-of-polymer/437/3 "2020-07-07T18:52:34Z")
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, ---
**Author:** ![mijiddorj](https://avatars.discourse-cdn.com/v4/letter/m/779978/32.png) [@mijiddorj](https://gromacs.bioexcel.eu/u/mijiddorj)\ **Post date:** [July 8, 2020, 3:21am UTC](https://gromacs.bioexcel.eu/t/cross-linking-of-polymer/437/4 "2020-07-08T03:21:16Z")
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. ---
**Author:** ![sako132002](https://avatars.discourse-cdn.com/v4/letter/s/a9adbd/32.png) [@sako132002](https://gromacs.bioexcel.eu/u/sako132002)\ **Post date:** [July 8, 2020, 4:04am UTC](https://gromacs.bioexcel.eu/t/cross-linking-of-polymer/437/5 "2020-07-08T04:04:52Z")
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, ---
**Author:** ![mijiddorj](https://avatars.discourse-cdn.com/v4/letter/m/779978/32.png) [@mijiddorj](https://gromacs.bioexcel.eu/u/mijiddorj)\ **Post date:** [July 8, 2020, 7:19am UTC](https://gromacs.bioexcel.eu/t/cross-linking-of-polymer/437/6 "2020-07-08T07:19:16Z")
I am sorry for that it is GROMACS forum. It should be discussed in AMBER mailing list. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [July 8, 2020, 2:25pm UTC](https://gromacs.bioexcel.eu/t/cross-linking-of-polymer/437/7 "2020-07-08T14:25:49Z")
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](http://manual.gromacs.org/documentation/current/reference-manual/topologies/pdb2gmx-input-files.html#special-bonds)