[gmx-users] EDITCONF question

[David L. Bostick]

Sorry,

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);
>         num++;
>         if(num % 15 == 0)
>                 printf("\n");
>         }
> }

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
> 
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> 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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