From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue Jan 04 2005 - 14:02:50 CST

O>>> "JS" == John Stone <johns_at_ks.uiuc.edu> writes:

JS> ops, I missed seeing Axel's reply. Axel's is a more
JS> complete answer, so I'd suggest starting with his suggestion.

it depends. since i don't usually have residue assignments
in car-parrinello simulations, i tend to forget about them
when you have them, using

'same resid as (name OW and within 20.0 of index 0)'

should be much faster in your case. with car-parrinello MD, you
cannot afford that many atoms, so one tends to get sloppy :-/

[...]

H>>> "VS" == VISWANADHA SRIDHARA <vsrid001_at_odu.edu> writes:

VS> i Axel and John,

VS> One more quick question, Here you mentioned keeping the whole molecule, if
VS> some of its atoms are within the range of the reference point, but what if
VS> it is the other way, if I Want to remove the entire molecule when some of
VS> its atoms are outside the range of the study of reference. Is it possible
VS> just by putting not(same residue as (within 20 of something)), after we
VS> select the pdb file.

ok, that is a little trickier. you have to carefully check the
and/or logic, but something like following (totally untested) might work:

'(same resid as (name OW and within 20.0 of index 0)) and not
same resid as (name HW1 HW2 and not within 20.0 of index 0)'

axel.

VS> Thanks in Advance.

--
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Axel Kohlmeyer       e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
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If you make something idiot-proof, the universe creates a better idiot.