On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Francesco Pietra wrote: >> >> Hello Sunny: >> I had already generated a valid .itp file for my protein using >> seq2itp. That .itp works for both the protein itself and the protein >> graphically inserted into a bilayer. When I add graphically further >> water it does not work any more. I thought there is something else >> that manages water without putting it everywhere. That script does not >> help. >> > > In order to get a solution to your problem, I think you're going to have to > explain your methodology more clearly, including command lines and actual > error messages. How are you adding water "graphically"? Is genbox not > working? Can you not simply grep for the number of water molecules, i.e.: > > grep W solvated.gro | wc -l > > and use that number in the topology? > > -Justin
I'll organize to explain in more details. The methodology (all-atoms) is explained in a few papers of mine and supplementary material, for example: F. Pietra “ Docking and MD simulations of the interaction of the tarantula peptide psalmotoxin‑1 with ASIC1a channels using a homology model” J. Chem. Inf. Model. 2009, 49, 972-977. thanks francesco > >> thanks >> francesco >> >> On Wed, Oct 21, 2009 at 3:46 PM, sunny mishra <mishra.su...@gmail.com> >> wrote: >>> >>> There is a seq2itp.pl script provided by martini folks in their >>> website. You can get it from there. >>> >>> Sunny >>> >>> On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra >>> <francesco.pie...@accademialucchese.it> wrote: >>>> >>>> Hi: >>>> I am looking for scripts that generate topology in coarse grained. >>>> Thanks for indications. >>>> >>>> francesco pietra >>>> _______________________________________________ >>>> gmx-users mailing list gmx-us...@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>>> >>> _______________________________________________ >>> gmx-users mailing list gmx-us...@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>> >>> >> _______________________________________________ >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > _______________________________________________ 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/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/mailing_lists/users.php
