Re: [AMBER] Asking for help: cross linking polymer

From: Dr. Anselm Horn <>
Date: Wed, 8 Jul 2020 09:56:29 +0200


to create multiple chains you could use the copy command in leap and
then use explicit commands to change the coordinates in a controlled
way. Finally, all chains are combined into a single unit and then saved
as a single system. Alternatively, you could use a molecular editor of
you choice to do that copy&translate graphically.
For the cross-linking, you have to specify the explicit atoms within the
different chains in the bond commands. (Have a look into the leap
section of the Amber manual.)

If you refer to disulfide bonds with the term "cross-linking", simply
use the known CYX residues for that, which are readily available within
the different Amber parameter sets.
In case you refer to (iso)peptide bonds, additional parameters are
needed, which are AFAIK not generally available. (However, I created a
working and consistent parameter set for peptide cross-linking via side
chains some time ago that still await publication - alas; if you are
interested in those, please let me know.)



On 07/08/2020 05:31 AM, SAKO MIRZAIE wrote:
> Thank you very much. How can I produce multiple chains of polymer by leap?
> (e.g. 20 chains). Then, how should I define the cross link between these
> chains? For the cross link, should I minimize the cross link residue by
> gaussian?
> Best,
> On Tue, Jul 7, 2020 at 9:42 PM David A Case <> wrote:
>> On Tue, Jul 07, 2020, SAKO MIRZAIE wrote:
>>> polymer has a cross- link and I don’t know how can I define the
>>> cross link by LEAP module in ambertools.
>> Use the "bond" command in tleap to define cross-links that you wish to add.
>> ...dac

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