-- Chandan kumar Choudhury NCL, Pune INDIA
On Fri, Aug 13, 2010 at 8:08 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > abdullah ahmed wrote: > >> Hello, >> >> I'd like to ask a question about the conversion of the results of >> minimization to pdb format. Here is what I do: >> >> 1. Apply pdb2gmx to the pdb file to convert it to .gro and .top >> (pdb2gmx -f -p -o) >> 2. Run editconf to define the box (editconf -d 1) >> 3. run gromp and mdrun for the minimization >> > use mdrun -c . It will give you the required pdb file Chandan > 4. Run editconf to re-convert back to pdb >> >> >> >> Unfortunately doing this seems to be adding some information into the pdb >> file that is not related to the atom coordinates. I think this might be >> trajectory data. Is there someway to remove this info? >> >> > What is it exactly that you're seeing? The output .gro file from mdrun > (which can be output as .pdb directly, if you prefer) contains only > coordinates and box vectors, so anything else should just be comment lines. > > -Justin > > > Thank you in advance, >> Abdullah >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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-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 >
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