[gmx-users] How to remove charge of 5e-2 ??
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Apr 6 14:16:59 CEST 2011
On 6/04/2011 10:03 PM, Hyunsik wrote:
> Thank you for your help.
>
> But if you don't mind can you tell me more specifically?
>
> Actually I don't know exactly what isolated protein system is.
The zwitterion option should only be used for a polypeptide of exactly
one residue, whose termini should be charged. Using the normal termini
perturbs the charge of the alpha-carbon. However separate
parametrization was done for the single-residue peptide case.
Mark
> hyun
> 2011. 4. 6., 오후 8:56, Justin A. Lemkul 작성:
>
>>
>> Hyunsik wrote:
>>> hm...
>>> is it possible that there is partial charge because of terminal of zwitterions?
>>> (NH3+ and COO-)
>>> When i tried to make system with terminal of just NH3+ and COO-, there was no partial charge like 5.00.
>>> But when i used zwitterion terminal, that made the 5.05 charge of the system..
>>> it can be happened? Or something weird?
>> The zwitterion option should only be used for isolated amino acids. If you have anything longer than a single residue (i.e. a polypeptide), you should not choose zwitterion-NH3+ or zwitterion-COO-, just the normal NH3+ and COO-.
>>
>> -Justin
>>
>>> Hyun
>>> 2011. 4. 6., 오후 5:00, Erik Marklund 작성:
>>>> mohsen ramezanpour skrev 2011-04-06 09.31:
>>>>>
>>>>> On Wed, Apr 6, 2011 at 11:53 AM, Erik Marklund <erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> No we don't. You can't have fractions of elementary particles in
>>>>> your molecules.
>>>>>
>>>>> Dear Erik
>>>>>
>>>>> Yes,You are right.It <http://right.It> is obvious .
>>>>> But I wanted to simulate a part of my system.for example a part of my protein!
>>>>> I was wrong,we can't do that
>>>>>
>>>> I think there are several examples of that in literature, e.g. by Åqvist and coworkers. But think they use a different approach than just cutting away part of the protein.
>>>>
>>>> Erik
>>>>> Erik
>>>>>
>>>>> mohsen ramezanpour skrev 2011-04-06 09.13:
>>>>>> Daer Dr.Mark
>>>>>>
>>>>>> You are right,But all of them(as I know) have integer charges!
>>>>>> the problem is simullating a system with partial charges.
>>>>>> We absolutely have such systems.
>>>>>>
>>>>>> On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham
>>>>>> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>>>>>
>>>>>> On 6/04/2011 4:45 PM, mohsen ramezanpour wrote:
>>>>>>> Dear Dr.Justin
>>>>>>>
>>>>>>> What can we do (how can neutralize system) if the total
>>>>>>> charge of our system was not integer?
>>>>>>> I think there is not any solution and we have to simulate
>>>>>>> a charged system not a neutral.
>>>>>>> Am I right?
>>>>>> I suspect every tutorial for simulating proteins in water
>>>>>> deals with the need for counter-ions, and the technique for
>>>>>> generating them.
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>>
>>>>>>> Thanks in advance
>>>>>>>
>>>>>>> On Wed, Apr 6, 2011 at 11:12 AM, mohsen ramezanpour
>>>>>>> <ramezanpour.mohsen at gmail.com
>>>>>>> <mailto:ramezanpour.mohsen at gmail.com>> wrote:
>>>>>>>
>>>>>>> Dear Dr.Justin
>>>>>>>
>>>>>>> I had the same problem.
>>>>>>> I modified the charges and charge groupsin the topology of a drug.the net charge of it is zero(I am sure)
>>>>>>> though,when I used pdb2gmx it resulted a NOTE like the
>>>>>>> following:
>>>>>>>
>>>>>>> NOTE:The system has non-zero total charge: 3.000003e00
>>>>>>> I continued simulation and ignored it!
>>>>>>> Because:
>>>>>>> 1- I checked my protein.top and qtot was 3
>>>>>>> 2-the net charge of my drug was 0
>>>>>>> 3-Besides,all charges have 3 digit precision,How can it
>>>>>>> have 0.000003 additional charge?!
>>>>>>>
>>>>>>> What is your point of view?
>>>>>>> Thanks in advance for your reply
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Apr 6, 2011 at 3:40 AM, Justin A. Lemkul
>>>>>>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 김현식 wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> > Date: Tue, 5 Apr 2011 23:43:19 +1000
>>>>>>> > From: Mark.Abraham at anu.edu.au
>>>>>>> <mailto:Mark.Abraham at anu.edu.au>
>>>>>>> > To: gmx-users at gromacs.org
>>>>>>> <mailto:gmx-users at gromacs.org>
>>>>>>> > Subject: Re: [gmx-users] How to remove
>>>>>>> charge of 5e-2 ??
>>>>>>> >
>>>>>>> > On 5/04/2011 11:17 PM, Hyunsik wrote:
>>>>>>> > > Dear experts,
>>>>>>> > >
>>>>>>> > > Hi,
>>>>>>> > >
>>>>>>> > > When prepare a system, the system had
>>>>>>> +5.5. So I add 5 CL- ion to neutralize.
>>>>>>> > >
>>>>>>> > > But as you know, the Cl charge is -1 and
>>>>>>> there still is 5e-2. how can i remove that.
>>>>>>> >
>>>>>>> > Your statements are inconsistent. If you had
>>>>>>> 5.5 charge and added five
>>>>>>> > chloride ions, you could not end up with 0.05.
>>>>>>>
>>>>>>> oh.. I have mistaken.. I had 5.005 of the
>>>>>>> system charge.
>>>>>>> So even if added five choride ions, the
>>>>>>> system charge is not zero. there was 0.005
>>>>>>>
>>>>>>> that is partial charge?? If like that,
>>>>>>> topology is broken or something wrong? abnormal??
>>>>>>>
>>>>>>>
>>>>>>> Maybe, maybe not. Rounding errors could account
>>>>>>> for this difference, especially if your system is
>>>>>>> very large. Still, you should inspect your
>>>>>>> topology/topologies for inconsistencies. If
>>>>>>> pdb2gmx created the topology, keep an eye on the
>>>>>>> "qtot" column for a running total of the charge.
>>>>>>> If you've made or adjusted any topologies on your
>>>>>>> own, double-check your work. If everything looks
>>>>>>> correct, then the difference is likely a
>>>>>>> consequence of floating-point math and nothing more.
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>>
>>>>>>> Thank you,
>>>>>>>
>>>>>>> Hyun
>>>>>>>
>>>>>>> >
>>>>>>> > Mark
>>>>>>> > --
>>>>>>> > gmx-users mailing list gmx-users at gromacs.org
>>>>>>> <mailto:gmx-users at gromacs.org>
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>>>>>>>
>>>>>>> -- ========================================
>>>>>>>
>>>>>>> Justin A. Lemkul
>>>>>>> Ph.D. Candidate
>>>>>>> ICTAS Doctoral Scholar
>>>>>>> MILES-IGERT Trainee
>>>>>>> Department of Biochemistry
>>>>>>> Virginia Tech
>>>>>>> Blacksburg, VA
>>>>>>> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>>
>>>>>>> ========================================
>>>>>>>
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>>>>>>>
>>>>>>
>>>>>> --
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>>>>>>
>>>>>
>>>>> -- -----------------------------------------------
>>>>> Erik Marklund, PhD student
>>>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>>>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>>>>> phone: +46 18 471 4537 fax: +46 18 511 755
>>>>> erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se> http://folding.bmc.uu.se/
>>>>>
>>>>>
>>>>> --
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>>>>>
>>>>
>>>> --
>>>> -----------------------------------------------
>>>> Erik Marklund, PhD student
>>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>>>> phone: +46 18 471 4537 fax: +46 18 511 755
>>>> erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
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>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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