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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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