----- Original Message ----- From: abdullah ahmed <abdullah_renk_ah...@hotmail.com> Date: Saturday, August 14, 2010 1:05 Subject: [gmx-users] editconf To: gmx <gmx-users@gromacs.org> ----------------------------------------------------------- |
> Hello, > > I'd like to ask a question about the conversion of the results of > minimization to pdb format. Here is what I do: > - > Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o) That's not quite the purpose of pdb2gmx. pdb2gmx generates the molecular topology in the .top file, and sanitizes the contents of the coordinate file, *by default* writing a .gro file. You could write this file in another format if you chose. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File - > Run editconf to define the box (editconf -d 1) - > run gromp and mdrun for the minimization - > Run editconf to re-convert back to pdb You can use mdrun -c confout.pdb to do this last step directly. > 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? I can't imagine what you mean. Did you use editconf on the .xtc or .trr file? In future, it's always a good idea to include your actual commands via copy-and-paste, else we are reduced to guessing whether you've done various things right or wrong, and that wastes our time and might not get you the help you need :-) Here, a small sample of the "unrelated" information might also have helped us understand the issue. Mark -- 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
