Hallo,
I found out the solution :
I forgot to give the program the atom-values.
To add them one has to close the SOL-chapter with QUI.
Best wishes,
Daniel
Make a water cap for a protein
0 0 0 0
XYZ
OMIT
XRAY
0 0 0 0
ABC
1 0
2 1.01 118.4 0.0 1 3
4 1.09 109.5 180.0 1 3
QUI
SOL
HW OW 4
0.41700 2.20 2.00
0 0 0 0
26.0 0.0 0.0 0.0
QUI
ATOM 1 2151
END
END
Daniel Wetzler wrote:
>Hallo there,
>
>
>I have a problem using EDIT on AMBER 5.
>If I use the following edit.in file I get the output below.Make a water
>cap for a protein
>I think I don't close the input in the right way. I also tried it with
>one or none END.
>Does anyone know how I can get edit running with my parameters ?
>
>
>Here's my edit.in :
>
>water-solute
>0 0 0 0
>XYZ
>OMIT
>XRAY
>0 0 0 0
>ABC
>1 0
>2 1.01 118.4 0.0 1 3
>4 1.09 109.5 180.0 1 3
>
>QUI
>SOL
>HW OW 4
>0.41700 2.20 2.00
>0 0 0 0
>26.0 0.0 0.0 0.0
>
>END
>END
>QUIT
>
>
>Here's the output :
>
>
>
>SOL:
>
>************************************************
>WATER MOLECULES WILL BE PLACED AROUND THE SOLUTE
>************************************************
>ANY WATER WITH AN OXYGEN DISTANCE LESS THAN 2.20 ANGSTROMS
>FROM THE SOLUTE WILL BE DISCARDED
>ANY WATER WITH A HYDROGEN DISTANCE LESS THAN 2.00 ANGSTROMS
>FROM THE SOLUTE WILL BE DISCARDED
>HYDROGEN CHARGE = 0.4170 OXYGEN CHARGE = -.8340
>ATOM TYPE FOR HYDROGEN = HW AND FOR OXYGEN = OW
>
>NUMBER OF 216WATER CUBES TO BE GENERATED = 4^3
>WATER MOLECULES WILL NOT BE REORIENTED
>ALL WATER MOLECULES GREATER THAN 26.00 ANGSTROMS
>FROM THE SOLUTE WILL BE DISCARDED
>There are 13824 water molecules initially considered
>10595 WATER MOLECULES ARE SOLVATING THE SOLUTE
>TOTAL CHARGE ON MOLECULE = 0.000
>
>*** EXTRA NEWLINE OR UNKNOWN KEYWORD:
>
>
>
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Received on Thu Oct 14 2004 - 13:53:00 PDT
