[gmx-users] a suitable forcefield for ions

[Nilkanta Chowdhury]

Hello team,

                how can I simulate a protein bind with FE4S4 in gromacs.
How to generate the topology.
Thank you..

On Wed, May 25, 2016 at 5:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/25/16 7:40 AM, mah maz wrote:
>
>> Thanks Justin. I can only find atoms in ffnonbonded.itp in Amber ff. Where
>> should I search for ions parameters in Amber ff?
>>
>>
> Every force field has an ions.itp file.  Look for those atom types.  But
> knowing those values won't really tell you anything on their own.  You need
> to know (1) the literature source of those parameters and (2) the pros/cons
> to those parameters, also in the literature.
>
> -Justin
>
> On Wed, May 25, 2016 at 4:01 PM, mah maz <mahmaz71 at gmail.com> wrote:
>>
>> Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can
>>> I use them for ions or they are already for ions?
>>> eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use
>>> thIS sigma and epsilon for Na+?
>>>
>>> On Wed, May 25, 2016 at 2:11 PM, mah maz <mahmaz71 at gmail.com> wrote:
>>>
>>> Hi all,
>>>>
>>>> i need forcefield parameters for ions. can anyone tell me which
>>>> forcefield contains ions? can i do ion simulations with amber ff?
>>>>
>>>> Thank you
>>>>
>>>>
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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