[gmx-users] EDITCONF question
David L. Bostick
dbostick at physics.unc.edu
Mon May 20 22:56:21 CEST 2002
Yes.. I've done this before with a simple parser like awk. You can tag all
the atom indices that are below or above a certain value of z and put the
indices in an index file. Then use editconf with the -n option. The awk
script should be something like this for index files.
if($8 < "a certain value")
# printf("ATOM %5d %-4s %3s %5d
if(num % 15 == 0)
David Bostick Office: 262 Venable Hall
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On Mon, 20 May 2002, Senthil Kandasamy wrote:
> I have a pdb file with a lipid monolayer and a water layer.
> The water layer is too thick and I want to remove half the waters from
> the system.
> I used editconf to center the box . Now, I need to remove all the waters
> with Z > a certain value. Can editconf do this?
> I tried to incorporate the PDB into excel and resorted the columns and
> deleted the appropriate entries. But when I finally save the pdb file as
> text, the formatting is all screwed up and editconf does not recognize
> the pdb file. It complains that there are zero atoms.
> IS there any other way to do this?
> how do people edit pdb files generally?
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