Hi Justin I tried several residue names, 1Ethylene, 1Eth but editconf says:
Program editconf, VERSION 4.5.4 Source code file: pdbio.c, line: 446 Software inconsistency error: Trying to deduce atomnumbers when no pdb information is present For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors What would be the correct format of pdb that is readable? Here is the pdb: 1Eth 1 C 0.672 -0.000 0.000 C 1Eth 2 C -0.672 -0.000 0.000 C 1Eth 3 H 1.238 -0.928 0.000 H 1Eth 4 H 1.238 0.928 0.000 H 1Eth 5 H -1.238 -0.928 0.000 H 1Eth 6 H -1.238 0.928 0.000 H Thanks On 1 April 2013 20:06, Justin Lemkul <[email protected]> wrote: > > > On 4/1/13 7:22 PM, Juliette N. wrote: > >> Hi all, >> >> I am trying to produce gro file from PDB file using editconf. >> >> Here is the pdb file >> >> HETATM 1 C 0.672 -0.000 >> 0.000 C >> HETATM 2 C -0.672 -0.000 >> 0.000 C >> HETATM 3 H 1.238 -0.928 >> 0.000 H >> HETATM 4 H 1.238 0.928 >> 0.000 H >> HETATM 5 H -1.238 -0.928 >> 0.000 H >> HETATM 6 H -1.238 0.928 >> 0.000 H >> >> Then I use: editconf -f X.pdb -o X.gro >> >> But the go file seems no to be correct >> >> 6 >> 0 C 1 0.067 -0.000 0.000 >> 0 C 2 -0.067 -0.000 0.000 >> 0 H 3 0.124 -0.093 0.000 >> 0 H 4 0.124 0.093 0.000 >> 0 H 5 -0.124 -0.093 0.000 >> 0 H 6 -0.124 0.093 0.000 >> 0.00000 0.00000 0.00000 >> >> Can anyone please help why this is happening? >> >> > And what exactly is wrong with it? You have no residue numbers or names > in the input .pdb file, so none appear in the .gro file. The coordinates > have been correctly transformed from Angstrom to nm within the limit of > precision. > > -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> > -- Thanks, J. N. -- 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
