[gmx-users] How to remove charge of 5e-2 ??
Hyunsik
nammika at hotmail.com
Wed Apr 6 14:03:30 CEST 2011
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.
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
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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/
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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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