[gmx-users] How to remove charge of 5e-2 ??

Hyunsik nammika at hotmail.com
Wed Apr 6 14:31:41 CEST 2011


oh.. i have missed it ...

Thank you, Justin and Mark.

it's really helpful for me.

Hyun 

2011. 4. 6., 오후 9:16, Justin A. Lemkul 작성:

> 
> 
> 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
>>>>>>>> 
>>>>>>>>               ========================================
>>>>>>>> 
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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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> 
> -- 
> ========================================
> 
> 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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