[gmx-users] How to remove charge of 5e-2 ??
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 6 14:16:18 CEST 2011
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.
>
If you're running pdb2gmx on a single amino acid, then some force fields have
special parameters for this zwitterion. If you have a polypeptide, use normal
(NH3+ and COO-) termini, not the special zwitterionic forms.
If this is still not clear, please post your pdb2gmx command line and any screen
output that indicates your choices for prompted input for specific comment.
-Justin
> 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
>>>>>>>
>>>>>>> ========================================
>>>>>>>
>>>>>>> -- gmx-users mailing list gmx-users at gromacs.org
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>>>>>>>
>>>>>>
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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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>>
>
>
--
========================================
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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