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 <er...@xray.bmc.uu.se >>>> <mailto:er...@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.abra...@anu.edu.au <mailto:mark.abra...@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.moh...@gmail.com >>>>>> <mailto:ramezanpour.moh...@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 >>>>>> <jalem...@vt.edu <mailto:jalem...@vt.edu>> wrote: >>>>>> >>>>>> >>>>>> >>>>>> 김현식 wrote: >>>>>> >>>>>> >>>>>> >>>>>> > Date: Tue, 5 Apr 2011 23:43:19 +1000 >>>>>> > From: mark.abra...@anu.edu.au >>>>>> <mailto:mark.abra...@anu.edu.au> >>>>>> > To: gmx-users@gromacs.org >>>>>> <mailto:gmx-users@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@gromacs.org >>>>>> <mailto:gmx-users@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-requ...@gromacs.org >>>>>> <mailto:gmx-users-requ...@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@gromacs.org >>>>>> <mailto:gmx-users@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-requ...@gromacs.org >>>>>> <mailto:gmx-users-requ...@gromacs.org>. >>>>>> Can't post? Read >>>>>> http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> <mailto:gmx-users@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-requ...@gromacs.org >>>>> <mailto:gmx-users-requ...@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 >>>> er...@xray.bmc.uu.se <mailto:er...@xray.bmc.uu.se> >>>> http://folding.bmc.uu.se/ >>>> >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> <mailto:gmx-users@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-requ...@gromacs.org >>>> <mailto:gmx-users-requ...@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 >>> er...@xray.bmc.uu.se http://folding.bmc.uu.se/ >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@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-requ...@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@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. 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