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#464 - 10/29/03 02:53 AM CHARMM error with RTF file
tjaart Offline
Forum Member

Registered: 10/16/03
Posts: 40
Loc: Pretoria, South Africa
I get the following errors when trying to open my rtf file for my ligand:

CHARMM> open unit 11 card read name ptp.rtf APPEND
VOPEN> Attempting to open::ptp.rtf::
OPNLGU> Unit 11 opened for APPEND access to ptp.rtf
**** Warning **** The following extraneous characters
were found while command processing in MISCOM
READ

CHARMM> read RTF card unit 11
MAINIO> Residue topology file being read from unit 11.
RDTITL> No title read.

***** LEVEL 1 WARNING FROM <RDTITL> *****
***** Title expected.
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5


***** LEVEL 0 WARNING FROM <RTFRDR> *****
***** Unexpected end of file during read
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5


What does it mean and how do I fix it? Any help will be appreciated!!

Thanks!!!!!
_________________________
Tjaart de Beer

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#465 - 10/29/03 10:37 AM Re: CHARMM error with RTF file [Re: tjaart]
cao Offline
Forum Member

Registered: 10/17/03
Posts: 23
How about:
open unit 11 read form name ptp.rtf
read RTF card unit 11 append

And, before above, add some title in your ptp.rtf.
Good luck!

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#466 - 10/29/03 12:57 PM Re: CHARMM error with RTF file [Re: cao]
tjaart Offline
Forum Member

Registered: 10/16/03
Posts: 40
Loc: Pretoria, South Africa
When I change my script as you said I only get an output file that stopped halfway.

Here is my input file:

*DHPS build file
*

! Read in Topology and Parameter files

open unit 1 card read name top_all22_prot.inp
close unit 1

open unit 1 card read name ptp_rtf.inp
close unit 1

open unit 1 card read name par_all22_prot.inp
close unit 1


! Read sequence from the PDB coordinate file
open unit 1 card read name pdb.pdb
close unit 1
generate prot setup

!LIG setup
open unit 1 card read name ptp.pdb
close unit 1
generate lig setup


! now generate the PSF and also the IC table (SETU keyword)
!generate
!pdb setup



!open unit 11 card read name ptp.psf APPEND
!read PARA card unit 11
!close unit 11


! read in pdb coordinate file
open unit 1 card read name pdb.pdb
read coor pdb unit 1
close unit 1

! build in hydrogens if using a crystal structure
hbuild sele all end

! build in missing coordinates using values in
! the parameter set
ic fill
ic para
ic build

! print all coordinates: undefined coordinates are indicated as
! 9999.00

print coor



! write out the protein structure file (psf) and
! the coordinate file in pdb format.

open write formatted unit 27 name pdb.psf
write psf card unit 27


open unit 1 card write name pdb_allh.pdb
write coor pdb unit 1

close unit 1

stop


-------------My ligand is called ptp. What is wrong?-------------

I get the following error message when running the script:

CHARMM> ! Read sequence from the PDB coordinate file
CHARMM> open unit 1 card read name pdb.pdb
VOPEN> Attempting to open::pdb.pdb::
OPNLGU> Unit 1 opened for READONLY access to pdb.pdb

CHARMM> close unit 1
VCLOSE: Closing unit 1 with status "KEEP"

CHARMM> generate prot setup
GENPSF> Segment 0 has been generated. Its identifier is ^@^@^@^@.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 0 Number of residues = 0
Number of atoms = 0 Number of groups = 0
Number of bonds = 0 Number of angles = 0
Number of dihedrals = 0 Number of impropers = 0
Number of HB acceptors = 0 Number of HB donors = 0
Number of NB exclusions = 0 Total charge = 0.00000
**** Warning **** The following extraneous characters
were found while command processing in CHARMM
PROT SETUP

CHARMM>

CHARMM> !LIG setup
CHARMM> open unit 1 card read name ptp.pdb
VOPEN> Attempting to open::ptp.pdb::
OPNLGU> Unit 1 opened for READONLY access to ptp.pdb

CHARMM> close unit 1
VCLOSE: Closing unit 1 with status "KEEP"

CHARMM> generate lig setup
GENPSF> Segment 0 has been generated. Its identifier is ^@^@^@^@.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 0 Number of residues = 0
Number of atoms = 0 Number of groups = 0
Number of bonds = 0 Number of angles = 0
Number of dihedrals = 0 Number of impropers = 0
Number of HB acceptors = 0 Number of HB donors = 0
Number of NB exclusions = 0 Total charge = 0.00000
**** Warning **** The following extraneous characters
were found while command processing in CHARMM
LIG SETUP

CHARMM>

CHARMM>


Help!!! How can I fix this??

Any help will be really appreciated!!!!!
Thanks!!!!!
_________________________
Tjaart de Beer

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#467 - 10/29/03 01:11 PM Re: CHARMM error with RTF file [Re: tjaart]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
You are not actually reading anything, your commands just open and close files.
(OPEN only establishes a connection between the unit number and the disk file, with some properties as specified - read/write, formatted/unformatted, ..., and you also have to explicitly perform some kind of I/O operation on that file in order to move data around)

Instead of:

open unít 11 read form name my_rtf.inp
read rtf form unit 11

you may want to ry the simpler syntax:

read rtf form name my_rtf.inp


This works for almost all read/write statements (one exception is when you read a sequence from a PDB file)
Use the example files in the Script Archive, and modify them to suit your needs!
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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