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.
-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
========================================
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