[gmx-users] editconf

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 13 17:08:26 CEST 2010

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
>    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.


> Thank you in advance,
> Abdullah


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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