[gmx-users] Re: Extracting the last frame of simulation into PDB

Justin Lemkul jalemkul at vt.edu
Fri Feb 15 21:25:01 CET 2013

On 2/15/13 3:22 PM, zugunder wrote:
> Oh, forgot about it completely... Thank you very much!
> BTW, is there any automated way to get rid of solvent molecules in PDB? I
> just need the structure for further manipulations (like mutations and adding
> several residues to the end). I do not find any options in editconf,
> deleting manually from PDB will take some time...

Create an index group that encompasses all non-solvent atoms (or whatever you 
like) and pass it to trjconv, then choose that group as the output.



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


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