Re: [AMBER] Two ion problem with

From: Pengfei Li <>
Date: Thu, 18 Aug 2016 21:18:35 -0400

Hi Abhilash,

You can use the checking method shown in the tutorial: <>. If there is nothing wrong with the parameters, it should be because there is only partial charge but no VDW parameters in the water hydrogen, in which situation you can use a restrained nonbonded model or a hybrid model (restrained nonboned model for the two waters + bonded model for the other metal ligating residues) to the simulation, as described in the end of the tutorial.

Kind regards,

> On Aug 18, 2016, at 3:17 PM, Abhilash J <> wrote:
> Hi!
> I tried and was successful in creating prmtop and inpcrd files. Thanks
> for the help. Gaussian was the only time taking step.
> But i am still unable to run the simulation.
> My system has 2 water molecules, a ligand and 1 residue (ASN) in
> co-ordinate bond with an ion.
> The problem is the water molecules come in clash with ASN during
> minimization. I tried different geometries (small changes) all in vain.
> I know it is the right starting geometry as it is reported in crystal
> structure.
> Please advice.
> On Tue, Aug 16, 2016 at 8:10 PM, Pengfei Li <>
> wrote:
>> 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,
>> Pengfei
>>> 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
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Received on Thu Aug 18 2016 - 18:30:02 PDT
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