Got this. Thank you
On Tue, Apr 16, 2013 at 11:21 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/16/13 5:32 AM, Steven Neumann wrote: > >> Thank you all. >> >> Would you suggest any link to a script like amb2gmx.pl ? I cannot fina >> anything like this - basically I wish to convert top.prmtop to top.tpr. >> >> >> > You will not be able to produce a .tpr file directly. The amb2gmx script > simply converts the prmtop to a .top file, which can then be input into > grompp. > > -Justin > > > >> >> On Tue, Apr 16, 2013 at 9:26 AM, francesco oteri >> <francesco.ot...@gmail.com>**wrote: >> >> Hi, >>> yes Marc you are right but the last time I used gromacs on a namd >>> trajectory >>> I noticed that time in the output files is useless 'cause it is always 0. >>> I understand that, since this information is usually took from .trr or >>> .xtc, it cannot >>> be extracted from a .dcd, but it could be more useful using as x the >>> frame >>> number. >>> This could, at least, permitting to visualize the plot with xmgrace >>> without >>> postprocessing >>> the .xvg >>> >>> >>> >>> Francesco >>> >>> >>> 2013/4/16 Mark Abraham <mark.j.abra...@gmail.com> >>> >>> On Apr 15, 2013 6:27 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: >>>> >>>>> >>>>> >>>>> >>>>> On 4/15/13 12:23 PM, Steven Neumann wrote: >>>>> >>>>>> >>>>>> Dear Gmx Users, >>>>>> >>>>>> I obtained dcd trajectory from simulation in another software. I wish >>>>>> >>>>> to >>> >>>> merge many trajectories using trjcat with a proper timestep. Is that >>>>>> >>>>> option >>>> >>>>> possible using gromacs or shall use a script to produce tpr file from >>>>>> >>>>> my >>> >>>> prmtop file e.g. amb2gmx ? Any links for such a script? >>>>>> >>>>>> >>>>> If you linked against VMD libraries when installing, Gromacs can handle >>>>> >>>> any trajectory/coordinate file format that VMD can, thus requiring no >>>> conversion. If you need a .tpr file to do the analysis you are trying to >>>> do, then yes, you need to convert topology information into the proper >>>> format. >>>> >>>> ...and be aware that a -s option that accepts both .tpr and (say) .gro >>>> formats (as shown in g_tool -h) might succeed with the latter if only >>>> >>> atom >>> >>>> names, rather than (say) bonding connectivity is required for g_tool to >>>> work. >>>> >>>> Mark >>>> >>>>> -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> * Please search the archive at >>>>> >>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >>>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> * Please search the archive at >>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >>>> >>>> >>> >>> >>> -- >>> Cordiali saluti, Dr.Oteri Francesco >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
