[gmx-users] EDITCONF question

David L. Bostick dbostick at physics.unc.edu
Mon May 20 22:56:21 CEST 2002

Hi ,

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
        printf("%-5d ",$2);
        if(num % 15 == 0)


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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