AMBER Archive (2002)

Subject: carnal

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri Dec 06 2002 - 17:47:56 CST

Hi,

I am trying to get a list of residues within a certain cutoff from the
center of mass of my structure (this should be similar to the biotin
tutorial, I know).
I am using the following input file for carnal

# CUTRES: list residues within cutoff of group
FILES_IN
  PARM p1 sph20.prmtop;
  STREAM s1 sph20.prmcrd;
FILES_OUT
DECLARE
  CUTRES c1 cmass 14.0;
OUTPUT
END

and the command
carnal < carnal.in> carnal.out

And I get the following error:

  CUTRES c1 cmass 14.0;
.................^
Error in stdin line 7: CUTRES: expected group id or coords of center
    Last token was cmass

I've tried various combinations, also using the following variant:

# CUTRES: list residues within cutoff of group
FILES_IN
  PARM p1 sph20.prmtop;
  STREAM s1 sph20.prmcrd;
FILES_OUT
DECLARE
  GROUP g1 cmass;
  CUTRES c1 g1 14.0;
OUTPUT
END

but nothing seems to work.

Anyone can explain better what is the correct usage of the groupid%....
examples in the manual?

Thank you,
Ioana

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