i am using the best conformation of protein ligand file obtained after docking results
i made the .gro file by pdb2gmx -f pro.pdb -o proceed.gro -water spc -missing -ignh then the ligand codinates from ligand,gro was obtained from prodrug sever, then i pasted ligand coordinates in this file the first three lines are Gallium Rubidium Oxygen Manganese Argon Carbon Silicon 2059 705SER N 1 -3.373 -1.131 1.295 705SER H1 2 -3.442 -1.166 1.232 705SER H2 3 -3.339 -1.043 1.261 705SER H3 4 -3.298 -1.196 1.303 last three lines are 1LIG OAR 33 0.425 -0.911 1.194 1LIG CAC 34 0.593 -1.073 1.167 1LIG CAT 35 0.500 -1.191 1.198 9.21266 2.49507 2.95990 and the output for command is wc -l proceed.gro 2100 proceed.gro On Wed, Jan 30, 2013 at 1:20 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/29/13 3:07 PM, amna khan wrote: > >> so, i could i correct this ? >> >> > Probably, but we need a lot more information if you want help: > > 1. Describe what your system is and how you constructed conf.gro > 2. Post the first 3 and last 3 lines of conf.gro > 3. Post the output of wc -l conf.gro > > -Justin > > >> >> On Wed, Jan 30, 2013 at 12:52 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 1/29/13 2:43 PM, az kalsom wrote: >>> >>> hi , >>>> >>>> when i use "editconf" to generate a dodecahedron box with the command >>>> >>>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0 >>>> >>>> the output shows the warning >>>> >>>> bad box in file >>>> >>>> generated a new cubic box 9.213 x 2.495 x 2.960 >>>> >>>> >>>> what is the mean of "bad box in file"? >>>> and why editconf generates a cubic box? >>>> >>>> >>>> Whatever input you have provided is malformatted. >>> >>> -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://vt.edu/Pages/Personal/justin> >>> <h**ttp://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> >>> <htt**p://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<h**ttp://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> >>> <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