[gmx-users] parameters problem

[Nidhi Katyal]

Thanks Justin. I would also like to know the reliability of parameters
generated using swiss param.


On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/10/14, 2:45 AM, Nidhi Katyal wrote:
>
>> Thank you Mark and Justin.
>> Now, I have carried out simulations using PME electrostatics and using
>> all other
>> parameters (except gromos 96 43a1 ff used) as suggested in
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>> gmx-tutorials/lysozyme/
>>
>> The protein is not loosing its structure now. But the problem is if I
>> carry out
>> simulations in the presence of experimentally known stabiliser generated
>> using
>> ProDrg (keeping all the parameters same while simulating both in the
>> presence
>> and absence of stabiliser), the partial loss of secondary structure is
>> observed
>> in the presence of stabilizer relative to the case in its absence at 350K
>> thereby implying simulations going against experimental observations
>> (although
>> slight stabilization was observed at 300K). Simulations were repeated
>> twice with
>> two different force fields.
>> However if I use above em,pr,full parameters with cut-off electrostatics,
>> although secondary structure is lost in the initial stages but I could
>> clearly
>> see the stabilization behaviour of additive in terms of secondary
>> structure
>> retainment till longer time. Is this observation a matter of chance-
>> reliable or
>> not? What could be the possible reason for not observing such
>> stabilization with
>> better parameters?
>>
>>
> Cutoff electrostatics are horribly inaccurate.  The fact that you
> conveniently see what you hope to when using a plain cutoff is likely by
> chance.
>
> The bigger issue is the use of PRODRG parameters.  As I have said numerous
> times on this list, the parameters it produces are demonstrably inaccurate
> and require reparametrization.
>
> http://pubs.acs.org/doi/abs/10.1021/ci100335w
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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