[gmx-users] protein complex

[Sana Saeed]

thank you Erik and Justin. i will read some papers and will start working. i will ask questions if get errors. thanks
Regards AutumnResearcherSoongsil University, South korea 


     On Tuesday, October 20, 2015 7:39 PM, Erik Marklund <erik.marklund at chem.ox.ac.uk> wrote:
   

 
> On 19 Oct 2015, at 23:44, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 10/19/15 9:56 AM, Sana Saeed wrote:
>> thanks for your reply. but i want to simulate it in gas phase. and i don't know
>> which steps to follow.
>> 
> 
> Vacuum protein simulations have been discussed recently; check the archives and try Google.  The protocol is simple.  Energy minimizaation, then a non-PBC simulation with zero cutoffs.  Whether or not there is an additive force field that can adequately model the gas phase is another story.  Additive biomolecular force fields overestimate gas-phase dipoles to mimic condensed-phase behavior.
> 
> -Justin

Compounding that is the difficulty of knowing which sites are protonated, which is very important in the gas phase. That said, there is a considerable bunch of papers about gas-phase proteins, how they pick up charge, and simulation studies of such systems.

On a technical note, I recommend gromacs 4.6.X for vacuum simulations, since the fast all-vs-all kernels were scrapped for 5.0. They will likely return at some point however, hopefully faster than ever.

Kind regards,
Erik

> 
>> 
>> 
>> On Monday, October 19, 2015 4:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 
>> 
>> 
>> 
>> On 10/19/15 1:21 AM, Sana Saeed wrote:
>> > i am working on complex of a protein , it has 5 chain and i want to simulate
>> the whole complex at the same time. can anyone help me in the procedure please.
>> 
>> >
>> 
>> It's no different than simulating a single protein.
>> 
>> -Justin
>> 
>> --
>> ==================================================
>> 
>> 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 <mailto:jalemkul at outerbanks.umaryland.edu> |
>> (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>> 
>> 
>> ==================================================
>> 
>> 
> 
> -- 
> ==================================================
> 
> 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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