Must be something wrong with my editor program (BBEdit), because when I open the file you sent me, it shows me there an additional blank line. Ok, time to switch to regular text editor…
Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:04 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/9/13 8:02 PM, Xu Dong Huang wrote: >> Oh, you have an Additional line after vector size box…. I thought you said >> to remove that blank line >> > > There is no additional line. The last line in the file must be the box > vectors. > > -Justin > >> Xu Dong Huang >> Chemical & Biochemical Engineering >> Rutgers School of Engineering >> xudo...@eden.rutgers.edu >> >> On Jan 9, 2013, at 7:58 PM, Xu Dong Huang <xudo...@eden.rutgers.edu> wrote: >> >>> @Justin, >>> >>> I did that, and it still says I have 103. >>> >>> Xu Dong Huang >>> Chemical & Biochemical Engineering >>> Rutgers School of Engineering >>> xudo...@eden.rutgers.edu >>> >>> On Jan 9, 2013, at 7:49 PM, Xu Dong Huang <xudo...@eden.rutgers.edu> wrote: >>> >>>> @Justin, >>>> >>>> I did what you suggested, and I still can't load my molecule in VMD. Maybe >>>> I am still doing something wrong with the new line character thing. >>>> >>>> >>>> Xu Dong Huang >>>> Chemical & Biochemical Engineering >>>> Rutgers School of Engineering >>>> xudo...@eden.rutgers.edu >>>> >>>> On Jan 9, 2013, at 7:22 PM, Xu Dong Huang <xudo...@eden.rutgers.edu> wrote: >>>> >>>>> @ Justin, >>>>> >>>>> I laughed. :) Thank you. I can't believe I miss the smallest and most >>>>> rudimentary things. >>>>> Thanks again, >>>>> Xu Dong Huang >>>>> Chemical & Biochemical Engineering >>>>> Rutgers School of Engineering >>>>> xudo...@eden.rutgers.edu >>>>> >>>>> On Jan 9, 2013, at 7:20 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>>> >>>>>> >>>>>> >>>>>> On 1/9/13 7:16 PM, Xu Dong Huang wrote: >>>>>>> @ Justin, >>>>>>> >>>>>>> Thanks for always saving me from my mistakes. But I don't quite >>>>>>> understand what is a new line character? >>>>>>> >>>>>> >>>>>> The thing you get when you press enter. >>>>>> >>>>>> http://en.wikipedia.org/wiki/Newline#In_programming_languages >>>>>> >>>>>> Note that Google has plenty more to say ;) >>>>>> >>>>>> There should not be a blank line at the end of the .gro file, though, >>>>>> but to be correctly parsed by VMD, the line must terminate with a '\n' >>>>>> character. So at the end of your box vector line, hit return then >>>>>> backspace. >>>>>> >>>>>> -Justin >>>>>> >>>>>> -- >>>>>> ======================================== >>>>>> >>>>>> Justin A. Lemkul, Ph.D. >>>>>> Research Scientist >>>>>> 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 >>>> >>>> -- >>>> 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 >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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
