Hi Abhilash,
You can use the checking method shown in the MCPB.py tutorial: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>. 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 MCPB.py tutorial.
Kind regards,
Pengfei
> On Aug 18, 2016, at 3:17 PM, Abhilash J <md.scfbio.gmail.com> 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 <ambermailpengfei.gmail.com>
> 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 MCPB.py 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 <sunita.bio.gmail.com>
>> wrote:
>>>
>>> Yes...in 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 complex.top and
>> complex.crd
>>>
>>> Hope it helps you
>>>
>>> On 12-Aug-2016 10:42 PM, "Abhilash J" <md.scfbio.gmail.com> 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
>>>> mcpb.py 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
