[gmx-users] EDITCONF question
David L. Bostick
dbostick at physics.unc.edu
Mon May 20 23:05:30 CEST 2002
I forgot to mention,.. this script is only for pdb files and let me clean
it up a bit to get..
> if($8 < "a certain value" && $1 == "ATOM")
> printf("%-5d ",$2);
> if(num % 15 == 0)
NOw, just put the value of z in for "a certain value" and call it like
awk -f file_w_the_above_script_in_it < in.pdb > out.ndx
then edit the out.ndx file by putting a tag at the top of the file to make
it a proper index file.. i.e. something like..
[ MY_ATOMS ]
> David Bostick Office: 262 Venable Hall
> Dept. of Physics and Astronomy Phone: (919)962-0165
> Program in Molecular and Cellular Biophysics
> UNC-Chapel Hill
> CB #3255 Phillips Hall dbostick at physics.unc.edu
> Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
> 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?
> > Thanks.
> > Senthil
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