[gmx-users] How to remove charge of 5e-2 ??
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 6 13:56:02 CEST 2011
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>
>>>>> >
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> > Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search
>>>>> before posting!
>>>>> > Please don't post (un)subscribe requests to
>>>>> the list. Use the
>>>>> > www interface or send it to
>>>>> gmx-users-request at gromacs.org
>>>>> <mailto:gmx-users-request at gromacs.org>.
>>>>> > Can't post? Read
>>>>> http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>> 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
>>>>> <mailto:gmx-users at gromacs.org>
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search
>>>>> before posting!
>>>>> Please don't post (un)subscribe requests to the
>>>>> list. Use the www interface or send it to
>>>>> gmx-users-request at gromacs.org
>>>>> <mailto:gmx-users-request at gromacs.org>.
>>>>> Can't post? Read
>>>>> http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> <mailto:gmx-users at gromacs.org>
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org
>>>> <mailto:gmx-users-request at gromacs.org>.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>>
>>>
>>>
>>> --
>>> -----------------------------------------------
>>> 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/
>>>
>>>
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>
>>
>> --
>> -----------------------------------------------
>> 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>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list