[gmx-users] simulation at acid medium

Tue Jul 8 16:55:09 CEST 2014

Hi Douglas
Thanks for you hints, that I
  will take into account.
I thank you very much the online
tool to protonate the aminoacids,
        Chris

Douglas Grahame <dgrahame at uoguelph.ca> ha escrito:

> 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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