[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
>>>>>>>> <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
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list 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
>
> ========================================
> --
> gmx-users mailing list 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
>
More information about the gromacs.org_gmx-users
mailing list