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Date: Fri, 27 Aug 2004 21:16:48 -0400
From: Vasiliy Znamenskiy <znamensk@sci.ccny.cuny.edu>
Subject: Re: Atom not found for quantum
In-reply-to: <AE6F7F4912065544BAF5BF75230925A164A72D@pnlmse23.pnl.gov>
To: "Vorpagel, Erich R" <Erich.Vorpagel@pnl.gov>
Cc: nwchem-users@emsl.pnl.gov
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Greetings Erich:

Thank you for your explanations.

However I don't understand your words about the 
modify-atom statement. I didn't specify the set in my 
input file.
I used following form: "modify atom 459:_OW quantum"

Following forms: "modify atom   459: OW    set 0 quantum" 
appear in the text of the output file as result of NwChem 
action.
Taking in attention your remark what I must do?
Must I specify the set explicitly, for example, by 1?
What is really the set?

Vasiliy

On Fri, 27 Aug 2004 14:11:54 -0700
  "Vorpagel, Erich R" <Erich.Vorpagel@pnl.gov> wrote:
>Greetings Vasiliy,
>
>In your modify atom statement, you have "set 0 quantum" 
>  Valid numbers
>for the "set" keyword are 1, 2 or 3.
>This is FORTRAN and not C so arrays start with 1 not 0.  
>
>Also quantum atoms need to be part of the solute and not 
>the solvent.
>Water molecule 495 is part of solvent because
>it has a fragment name HOH.  You need to copy the HOH.frg 
>file and
>create a WAT.frg file and then include the water molecule 
>as part of the
>solute in the initial pdb file.
>
>Erich R. Vorpagel, Ph.D.     Chief Scientist
>MSCF Visualization and User Services Group 
>Environmental Molecular Sciences Laboratory
>Pacific Northwest National Laboratory  
>P. O. Box 999,  MS: K8-91
>3335 Q Ave.                                  Phone: 
> 509-376-0751
>Richland, WA  99352                     FAX: 
>     509-376-0420
>Email: erich.vorpagel@pnl.gov      Cell Ph: 509-531-6226
>Web:  http://mscf.emsl.pnl.gov/
>
>
>
>-----Original Message-----
>From: owner-nwchem-users@emsl.pnl.gov
>[mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of 
>Vasiliy Znamenskiy
>Sent: Friday, August 27, 2004 4:13 AM
>To: nwchem-users@emsl.pnl.gov
>Subject: Atom not found for quantum
>
>
>Hi,
>
>Last strings of output file
>/home/vasily/ac62p4z4qttw/ac62p4z4qttw.output.145687 look 
>like following:
>
>   modify atom    21:2HE2   set 0 quantum
>   modify atom    21: NE2   set 0 quantum
>   modify atom    21: OE1   set 0 quantum
>   modify atom    21: CD    set 0 quantum
>   modify atom    21:3HG    set 0 quantum
>   modify atom    21:2HG    set 0 quantum
>   modify atom    21: CG    set 0 quantum
>   modify atom   459: OW    set 0 quantum
>
>  
>************************************************************************
>*********
>******
>   *   0: Atom not found for quantum    0
>       *
>  
>************************************************************************
>*********
>******
>0:0::: 0
>prun: /scratch/nwchem (host m565 process 0 pid 6103) 
>killed by signal 11 (SEGV)
>
>
>I have checked the initial pdf file 
>/home/vasily/ac62p4z4qttw/ac62p4z4qttw.pdb . There are 
>following strings:
>
>ATOM   1814  OW  HOH   459       2.130  -2.130  -3.910
>ATOM   1815 2HW  HOH   459       1.970  -1.360  -3.300
>ATOM   1816 3HW  HOH   459       2.970  -2.600  -3.650
>
>Atom   OW  HOH   459  exists.
>
>Which atom not found for quantum? 
>Thank you.
>