Re: [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  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  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  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

jalem...@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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [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  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  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  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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] a suitable forcefield for ions

[Justin Lemkul]

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  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  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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] a suitable forcefield for ions

[mah maz]

Thanks Justin. I can only find atoms in ffnonbonded.itp in Amber ff. Where
should I search for ions parameters in Amber ff?

On Wed, May 25, 2016 at 4:01 PM, mah maz  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  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
>>
>
>
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Re: [gmx-users] a suitable forcefield for ions

[Justin Lemkul]

On 5/25/16 7:31 AM, mah maz 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+?



You should spend some time in the literature; there is a long history of ion 
parametrization and refinement, with subsequent discussion of which parameters 
are best for what application.  This is not an issue that is solved simply by 
perusing GROMACS force field files.


All of the force fields in GROMACS have ion parameters; it's up to you to decide 
which, if any, of these is suitable for whatever type of simulation(s) you want 
to do.


-Justin


On Wed, May 25, 2016 at 2:11 PM, mah maz  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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] a suitable forcefield for ions

[mah maz]

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  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
>
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Re: [gmx-users] a suitable forcefield for ions

[Erik Marklund]

Hi,

Which ions? The monovalent ions commonly used with Amber have a tendency to 
cluster in unrealistic ways at moderate concentrations if memory serves me 
right.

Kind regards,
Erik

> On 25 May 2016, at 10:41, mah maz  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
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
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[gmx-users] a suitable forcefield for ions

[mah maz]

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
-- 
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