Hi if you found optimum size for your protein , you must use VMD ---> Tk console , I done it
for commands, please see manual of VMD or mailing list. Best Regards Hamid Mosaddeghi ________________________________ From: Tsjerk Wassenaar <tsje...@gmail.com> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Saturday, 16 February 2013, 13:19 Subject: Re: [gmx-users] calculate the size of protein Hi KT, If you set a box in any way, editconf writes the size of the box in the input file, the dimensions of the system and the size of the resulting box. Cheers, Tsjerk On Sat, Feb 16, 2013 at 10:42 AM, Kieu Thu Nguyen <kieuthu2...@gmail.com> wrote: > Hi, > > What is the specific editconf command should i use to calculate the > dimensions of fitting box of the protein ? > > Thanks and regards, > KT > > > On Fri, Feb 8, 2013 at 2:03 PM, Kieu Thu Nguyen <kieuthu2...@gmail.com>wrote: > >> Thank Tsjerk ! I mean that i want to determine the dimensions (x, y, z) of >> the protein >> >> >> On Fri, Feb 8, 2013 at 1:48 PM, Tsjerk Wassenaar <tsje...@gmail.com>wrote: >> >>> Hi KT, >>> >>> What do you mean with size? >>> >>> - circumscribed radius: editconf >>> - radius of gyration: g_gyrate >>> - dimensions of fitting box: editconf >>> - volume: g_sas >>> >>> Cheers, >>> >>> Tsjerk >>> >>> On Fri, Feb 8, 2013 at 5:55 AM, Kieu Thu Nguyen <kieuthu2...@gmail.com >>> >wrote: >>> >>> > Dear all, >>> > >>> > I want to calculate the size of the protein. Which tool should i use for >>> > this purpose ? >>> > >>> > Thanks and regards, >>> > KT >>> > -- >>> > 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 >>> > >>> >>> >>> >>> -- >>> Tsjerk A. Wassenaar, Ph.D. >>> >>> post-doctoral researcher >>> Biocomputing Group >>> Department of Biological Sciences >>> 2500 University Drive NW >>> Calgary, AB T2N 1N4 >>> Canada >>> -- >>> 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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
