Thanks for your reply.
The problem which I have posted before in that the sphere will play the
role of inert (i.e. only vdw interactions) crowders for the macromolecule
of interest. Each sphere should have a radius of (say) 50 Angs. The spheres
are supposed to mimic the effect of inert crowders like Ficoll.
*Atul Kuamr jaiswal*
Research Scholar
School of Computational and Integrative Sciences
Centre for Computational Biology and Bioinformatics (CCBB)
JNU,New Delhi
India.
On Wed, Nov 12, 2014 at 12:00 PM, ATUL KUMAR <atul44_sit.jnu.ac.in> wrote:
> The spheres will play the role of inert (i.e. only vdw interactions)
> crowders for the macromolecule of interest. Each sphere should have a
> radius of (say) 50 Angs. The spheres are supposed to mimic the effect of
> inert crowders like Ficoll.
>
>
> On Tue, Nov 11, 2014 at 5:17 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>> On Tue, Nov 11, 2014, ATUL KUMAR wrote:
>>
>> > I want to represent a molecule with a sphere and my system would be a
>> > macromolecule + spheres. Spheres have only Van der waals interaction, no
>> > charge and it does not make any covalent bond. So, I need to put only
>> mass
>> > and VDW parameters for the sphere in AMBER. I am trying to find a good
>> set
>> > of vdw parameters for my sphere. Has anybody done like this? Any pointer
>> > would be appreciated.
>>
>> I don't think anyone could answer this question without knowing what the
>> spheres are supposed to represent.
>>
>> ....dac
>>
>>
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>>
>
>
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Received on Thu Nov 13 2014 - 04:30:02 PST
