[gmx-users] editconf

Mark Abraham mark.abraham at anu.edu.au
Sat Aug 14 02:36:20 CEST 2010

----- Original Message -----
From: abdullah ahmed <abdullah_renk_ahmed at hotmail.com>
Date: Saturday, August 14, 2010 1:05
Subject: [gmx-users] editconf
To: gmx <gmx-users at gromacs.org>

> 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.


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