[gmx-users] a suitable forcefield for ions

[Justin Lemkul]

On 5/25/16 8:49 AM, Nilkanta Chowdhury wrote:
> Hello team,
>
>                 how can I simulate a protein bind with FE4S4 in gromacs.
> How to generate the topology.

Please start a new thread if you have an unrelated question, rather than 
hijacking someone else's topic.

This question has come up before; I don't know if there are good force fields 
for such species due to the complexity of their nature.  Try Google.

-Justin

> 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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-- 
==================================================

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

==================================================