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 <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 >>> > > -- > ======================================== > > 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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