[gmx-users] parameters problem

[Justin Lemkul]

On 3/10/14, 8:21 AM, Nidhi Katyal wrote:
> Thanks Justin. I would also like to know the reliability of parameters
> generated using swiss param.
>
>

I have no personal experience with it.  My rule is to never trust anything from 
a black-box server without verifying it and assessing any information about 
penalties, deviations, etc. that it provides.

-Justin

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

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

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