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#15523 - 09/12/07 09:16 AM "Cannot append to full set" - reading in a PDB
haydnw Offline
Forum Member

Registered: 04/25/06
Posts: 6
Hi,

I'm trying to read in a PDB to orient two structures. However, when I try to read in the first set of coordinates, CHARMM falls over with the message "Cannot append to full set". I'd be grateful for any possible suggestions people may have as to why this might be happening.

CHARMM input file (extract):
Code:
!********************************************************
! Get PDB files to be oriented
!*********************************************************
OPEN UNIT 1 READ FORMatted NAME @FILE1
READ COORdinates PDB UNIT 1
CLOSe UNIT 1
OPEN UNIT 2 READ FORMatted NAME in/1ayg.pdb.helix1.pdb
READ COORdinates PDB UNIT 2
COORdinates COPY SELEction TYPE CA END COMParison
CLOSe UNIT 2



CHARMM output file (extract):
Code:
CHARMM>    !********************************************************
CHARMM> ! Get PDB files to be oriented
CHARMM> !*********************************************************
CHARMM> OPEN UNIT 1 READ FORMatted NAME @FILE1
Parameter: FILE1 -> "1A7W.PDB.HELIX1.PDB"
VOPEN> Attempting to open::1a7w.pdb.helix1.pdb::
OPNLGU> Unit 1 opened for READONLY access to 1a7w.pdb.helix1.pdb

CHARMM> READ COORdinates PDB UNIT 1
SPATIAL COORDINATES BEING READ FROM UNIT 1

***** LEVEL 0 WARNING FROM <COORIO> *****
***** Cannot append to full set
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5



PDB file format:
Code:
ATOM      1  N   ILE     1      -5.775  -1.911   0.247  1.00 31.76           N  
ATOM 2 CA ILE 1 -6.237 -3.077 0.991 1.00 33.46 C
ATOM 3 C ILE 1 -5.512 -4.373 0.711 1.00 33.01 C
ATOM 4 O ILE 1 -5.372 -5.209 1.589 1.00 31.67 O
...
ATOM 74 CG ASP 10 2.524 -12.907 4.136 1.00 44.18 C
ATOM 75 OD1 ASP 10 2.201 -13.616 3.159 1.00 41.52 O
ATOM 76 OD2 ASP 10 3.150 -11.781 4.093 1.00 47.20 O
TER 77 ASP 10
END


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#15524 - 09/12/07 09:25 AM Re: "Cannot append to full set" - reading in a PDB [Re: haydnw]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4742
Loc: ~ 59N, 15E
Don't post extracts. Construct a minimal but complete input file that shows the problem.
As to you problem: My guess is that you don't have a psf, but this is of course not clear from you extract.
When you solve this your next problem will be that the second read destroys the coordinates already present. Either do the copy before the second read or add the COMP keyword to one of the read coor statements:

* A complete example. CHARMM coordinate files are recommended for CHARMM use
*
read rtf card name my.rtf
read para card name my.prm
read psf card name my.psf
read coor card name file1.crd
read coor card name file2.crd comp
coor orie rms sele .... end
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#15525 - 09/12/07 10:43 AM Re: "Cannot append to full set" - reading in a PDB [Re: lennart]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8379
Loc: 39 03 48 N, 77 06 54 W
A common cause of this error is failure to READ or GENErate a PSF prior to reading coordinates.

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Moderator:  John Legato, lennart