yes i have following this tutorial , the only difference i made is that i didn't change the charges for ligand file.
it seems it is necessary to do this ? am i rite ? On Wed, Jan 30, 2013 at 1:51 AM, Justin Lemkul <[email protected]> wrote: > > > On 1/29/13 3:46 PM, amna khan wrote: > >> 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, >> > > Beware the quality of PRODRG topologies - they are never sufficiently > accurate without manual reparameterization. Using the coordinates from > PRODRG may or may not cause problems. Make sure you don't allow PRODRG to > run EM on the structure, or else the docked pose will be altered. > > > 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 >> >> > This shows your problem. You didn't account for the fact that you pasted > in a ligand by properly incrementing the atom count on the second line of > the file. Thus, when editconf reaches atom 2059, it expects to find box > vectors on the next line, but instead finds another atom and gives you the > "bad box" message. Your file actually has 2097 atoms (2100 - 3). > > Note that there is a protein-ligand tutorial available if these concepts > are unfamiliar to you. > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** > gmx-tutorials/complex/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html> > > -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 [email protected] > 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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
