On 6/04/2011 10:03 PM, 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.
The zwitterion option should only be used for a polypeptide of exactly one residue, whose termini should be charged. Using the normal termini perturbs the charge of the alpha-carbon. However separate parametrization was done for the single-residue peptide case. Mark > 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. 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