[gmx-users] simulation at acid medium
Douglas Grahame
dgrahame at uoguelph.ca
Mon Jul 7 18:30:00 CEST 2014
Hi Chris,
I'm not sure if this is what you need specifically but I've been
looking at protein denaturation in acidic and alkaline medium and the
strategy that I've come up with is to generate a pdb file with the correct
protonation state using this online tool (http://biophysics.cs.vt.edu/).
>From there I've been running a 'standard' simulation for 50 - 100ps using
the amber99sbnmr1-ildn force field. Although the choice of force field is
application specific and the time should be tailored to your project
specifically as well I'm hoping that this gives me an appropriate data set
to look at structural changes. Although this doesn't take into account an
acidic medium it should still hopefully provide structural data, I've also
been looking into constant pH simulations or trying to play around with the
H++ concentration in the medium but I've been running into more challenges
than I expected.
To be honest not entirely sure if this is the best means of going about it
either so if anyone else has any suggestions or alternative I'd love to hear
them as well! Cheers and hope that helps,
-Douglas Grahame
BSc. MSc. PhD. Candidate
dgrahame at uoguelph.ca
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
donna at iflysib.unlp.edu.ar
Sent: July 7, 2014 10:46 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] simulation at acid medium
Hi Erik
Thanks for your hints
Sorry, I have problems with internet, so I could not answer you before
I thought something was wrong with the MD simulation at physiological
solution since it looks like as a MD simulation at water. But I did not
take into account the protonation states!!!
Please, do you Know any another form to have acid medium?.
thanks again,
Chris
Erik Marklund <erik.marklund at chem.ox.ac.uk> ha escrito:
> Then you essentially need to protonate the side chains according to
> their pKa and the pH. Note that the protons will not hop around
> between groups in normal MD. What makes you think something's wrong
> with your physiological solution?
>
> Kind regards,
> Erik
>
>
> On 4 Jul 2014, at 19:47, donna at iflysib.unlp.edu.ar wrote:
>
>> Hi Erik
>>
>> Thanks.
>> Details:
>> System: proteins
>> Properties: those ones for which there are analyzes tools in Gromacs
>>
>> I am trying to model some proteins at acid medium.
>> I use MD with water and I create a physiological solution from the
>> counterion tool of Gromacs, But I think something is wrong.
>>
>> To analize properties: I use RMSD of alfa carbons to test the
>> converge of the MD. Also the idea is to analyze the giration radii
>> and the fluctuations through the Raddi of Giration and the RMSDF
>> tools that gives Gromacs.
>>
>> I realize now that Ia use the neutral protonate states for the
>> proteins when I use the physiological solution, and this is an
>> error. So, the results in RMSD, RG and RMSDF should be different
>> from those that I have now.
>> Sorry, I'm not a chemistry nor a biochemistry. I am a physics, so I
>> have some missing concepts.
>>
>> Kind regards
>> Chris
>>
>> I do not known if it is another different way to do the medium
>>
>> Erik Marklund <erik.marklund at chem.ox.ac.uk> ha escrito:
>>
>>> Hi Chris,
>>>
>>> This very much depends on what system you are studying and what
>>> properties you aim to look at. Could you provide more detail please.
>>>
>>> Kind regards,
>>> Erik
>>>
>>> Erik Marklund, PhD
>>> Postdoctoral Research Associate
>>>
>>> Department of Chemistry
>>> Physical & Theoretical Chemistry Laboratory University of Oxford
>>> South Parks Road Oxford
>>> OX1 3QZ
>>>
>>> On 4 Jul 2014, at 16:45, donna at iflysib.unlp.edu.ar wrote:
>>>
>>>> Dear all
>>>> Please, I need help.
>>>> I have to do a simulation at an acid medium (PH = around 5 or 6).
>>>> Is it sufficient to work with normal water,from it to create a
>>>> physiological solution (Ph=around 5) and then to work with the
>>>> physiological solution?
>>>> I would very much appreciate any clues in this regards
>>>>
>>>> Chris
>>>>
>>>> Dra. M. Cristina Donnamaria
>>>> Instituto de Fisica de Liqidos y Sistemas Biologicos
>>>> -IFLYSIB-
>>>> Comision de Invegtigaciones Cientificas de la Prov.
>>>> de Bs. As. Argentina
>>>>
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