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? 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> wrote: >> Hi, >> >> No we don't. You can't have fractions of elementary particles in your >> molecules. >> >> Dear Erik >> >> Yes,You are 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> >>> 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> 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> wrote: >>>> >>>> >>>> 김현식 wrote: >>>> >>>> >>>> > Date: Tue, 5 Apr 2011 23:43:19 +1000 >>>> > From: mark.abra...@anu.edu.au >>>> > To: 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 >>>> > 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. >>> 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 >> 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 >> > > > -- > ----------------------------------------------- > 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 > 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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
