Re: [AMBER] Two ion problem with

From: Pengfei Li <>
Date: Tue, 16 Aug 2016 10:40:46 -0400

Hi Abhilash,

Since it is a homo dimmer, you can parameterize a monomer and use the generated parameters for both monomers. You can treat the two active site with the same parameter set, in which way you need to manually rename the active site residues on the other monomer (other than the one used for parameterization) according to the new residue names generated for the active site residues of the monomer you have parameterized. Also you need to mirror the related commands “e.g. bond commands” in the tleap input for the other monomer.

You can also prepare the two monomer system separately and finally use the combine command to combine them (like sunita said).

Kind regards,

> On Aug 12, 2016, at 3:50 PM, sunita guptacDgug <> wrote:
> tleap we can combine many molecules together to make a complex.
> Eg. Load protein as x variable..1st ligand as y and 2nd ligand as z. Later
> combine x y z as another variable and save it as and complex.crd
> Hope it helps you
> On 12-Aug-2016 10:42 PM, "Abhilash J" <> wrote:
>> Hi everyone!
>> I need to prepare a homo dimer system with each monomer having a ligand
>> and a metal ion in its active site.
>> Both active sites are far from each other and don't affect each other
>> directly.
>> I think I will be able to prepare the one active site at a time using
>> tutorial. (I have gone through the tutorial)
>> How is it possible to prepare the complete complex (2 monomers with
>> their respective ions and ligands) together?
>> Is it possible to prepare the system one active site at a time and join
>> them together to complete the system.
>> Please advice.
>> Regards
>> _______________________________________________
>> AMBER mailing list
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Received on Tue Aug 16 2016 - 08:00:03 PDT
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