To all carnal specialists:
I'm studyin a protein-peptide complex. The protein is 101 aa long
(numbered 1 to 101), the peptide is 8 aa long (numbered 102 to 109). I'm
trying to generate a list of residues within 10. Angstroms from the
peptide, by using the following carnal input:
FILES_IN
PARM p1 /disk1/nachman/yeeia_new.top;
STREAM s1 /disk1/nachman/yeeia_new.crd;
FILES_OUT
TABLE t1 table.cutres;
DECLARE
GROUP grpid (RES 102-109);
CUTRES id grpid 10.0;
OUTPUT
TABLE t1 id%residues;
END
What I get is:
- CARNAL -
AMBER 6.0
COORDINATE ANALYSIS
input stdin
> FILES_IN
> PARM p1 /disk1/nachman/yeeia_new.top;
Reading parm file (/disk1/nachman/yeeia_new.top)
parm: opening /disk1/nachman/yeeia_new.top
/disk1/nachman/yeeia_new.top title:
> STREAM s1 /disk1/nachman/yeeia_new.crd;
Using default parm (/disk1/nachman/yeeia_new.top) for STREAM s1
stream: opening /disk1/nachman/yeeia_new.crd
> FILES_OUT
> TABLE t1 table.cutres;
> DECLARE
> GROUP grpid (RES 102-109);
** Group grpid: 135 atoms
> CUTRES id grpid 10.0;
list of residues at least partially in group:
102 103 104 105 106 107 108 109
> OUTPUT
> TABLE t1 id%residues;
TABLE t1 id%residues;
............^
Error in stdin line 10: TABLE: wrong type of item
Last token was id
There seem to be two problems:
(1) CUTRES selects only the peptide residues
(2) What do I have to specify in the TABLE line in the OUTPUT section?
Thanks in advance,
Joseph
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Joseph Nachman Department of Biochemistry
nachman_at_hera.med.utoronto.ca University of Toronto
Medical Sciences Building
tel: +1 416 978-5510 Toronto, Ontario M5S 1A8
fax: +1 416 978-8548 Canada
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Received on Fri Mar 16 2001 - 11:58:45 PST
