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problem in generating RNA
#1547 06/01/04 11:35 AM
Joined: Nov 2003
Posts: 68
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Posts: 68
i am trying to generate .psf and .crd files from an rna .pdb file.
for simplicity, i am using a .pdb file for a single ADE nucleotide.
i'm having some trouble, with the warning "** WARNING ** For atom in coordinate file, could not find residue in PSF, and is thus ignored:
"
and later , all the atoms were moved to 9999.000009999.000009999.00000 and the whole procedure crashed.
can anyone tell me what's going on?
thanks,
t.
my input file is:
"
! Open and read the topology and parameter files

read rtf card name top_all27_na.inp

read param card name par_all27_na.inp
set seg 1
! Read Sequence
OPEN READ UNIT 13 CARD NAME "ADE.pdb"
READ SEQUENCE PDB UNIT 13
! generate segment mysp30 and set up internal coordinate table
GENERATE RNA1 SETUP
! rewind the protein data bank file for reading for reading of coordinates
REWIND UNIT 13
! read the pdb coordinates
READ COORDINATES PDB UNIT 13
CLOSE UNIT 13
! print coordinates to output file missing coordinates
! (hydrogens) are asigned values of 9999.0
PRINT COORDINATES
! construct hydrogen positions
HBUILD
! print coordinates to output file . all hydrogen
! positins constructed
PRINT COORDINATES
! if necessary , any additional missing coordinates
! can be placed using the following commands
IC FILL PRESERVE
IC PARAMETERS
IC BUILD
! write the coordinates to a disk file
OPEN WRITE UNIT 14 CARD NAME RNA_@seg.CRD
WRITE COORDINATES CARD UNIT 14
OPEN WRITE UNIT 15 CARD NAME RNA_@seg.PSF
WRITE PSF CARD UNIT 15
* crn coordinates
* heavy atom positions taken from pdb
*
STOP

"


the pdb file is
"
HEADER


ATOM 3576 P ADE 0 167 35.124 163.439 96.680 1.00 34.30 P
ATOM 3577 O1P ADE 0 167 36.547 163.028 96.802 1.00 34.30 O
ATOM 3578 O2P ADE 0 167 34.660 164.112 95.440 1.00 34.30 O
ATOM 3579 O5' ADE 0 167 34.209 162.156 96.920 1.00 34.30 O
ATOM 3580 C5' ADE 0 167 34.665 160.861 96.551 1.00 34.30 C
ATOM 3581 C4' ADE 0 167 34.917 160.028 97.784 1.00 34.30 C
ATOM 3582 O4' ADE 0 167 33.651 159.695 98.414 1.00 34.30 O
ATOM 3583 C3' ADE 0 167 35.574 158.686 97.515 1.00 34.30 C
ATOM 3584 O3' ADE 0 167 36.988 158.839 97.462 1.00 34.30 O
ATOM 3585 C2' ADE 0 167 35.127 157.865 98.717 1.00 34.30 C
ATOM 3586 O2' ADE 0 167 35.878 158.145 99.882 1.00 34.30 O
ATOM 3587 C1' ADE 0 167 33.689 158.359 98.892 1.00 34.30 C
ATOM 3588 N9 ADE 0 167 32.718 157.581 98.122 1.00 34.30 N
ATOM 3589 C8 ADE 0 167 32.583 157.541 96.755 1.00 34.30 C
ATOM 3590 N7 ADE 0 167 31.612 156.767 96.342 1.00 34.30 N
ATOM 3591 C5 ADE 0 167 31.070 156.261 97.513 1.00 34.30 C
ATOM 3592 C6 ADE 0 167 30.004 155.388 97.749 1.00 34.30 C
ATOM 3593 N6 ADE 0 167 29.265 154.867 96.776 1.00 34.30 N
ATOM 3594 N1 ADE 0 167 29.718 155.072 99.030 1.00 34.30 N
ATOM 3595 C2 ADE 0 167 30.460 155.616 100.002 1.00 34.30 C
ATOM 3596 N3 ADE 0 167 31.486 156.460 99.907 1.00 34.30 N
ATOM 3597 C4 ADE 0 167 31.744 156.746 98.618 1.00 34.30 C

END
"

the .out file is
"/msi98/msi2001/biosym_bin/charmm cmd=' charmm.exe '
1
Chemistry at HARvard Macromolecular Mechanics
(CHARMm) - Version 29.1 Revision: 2002.1029
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: IRIX64-6.5(IP30)@ribosr.weizmann.ac.il
Created on Tue Jun 1 14:08:06 2004 by user: assaz

Maximum number of ATOMS: 60000, and RESidues: 72000
Current HEAP size: 10240000, and STACK size: 2000000

Checked out license feature: CHARMM_TokenR [for 753:78109:8:THE WEIZMANN INSTITUTE OF SCIENCE] (4 copies of MSI_TokenR)

RDTITL>
RDTITL> No title read.

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


CHARMM>

CHARMM> read rtf card name top_all27_na.inp
VOPEN> Attempting to open::top_all27_na.inp::
MAINIO> Residue topology file being read from unit 90.
TITLE> * \\\\ CHARMM27 ALL-HYDROGEN NUCLEIC ACID TOPOLOGY FILE ////
TITLE> * \\\\\\\\\\\\\\\\\\ DEVELOPMENTAL ////////////////////////
TITLE> * ALEXANDER D. MACKERELL JR. AND NICOLAS FOLOPPE
TITLE> * AUGUST 1999
TITLE> * ALL COMMENTS TO ADM JR. EMAIL: ALEX,MMIRIS.AB.UMD.EDU
TITLE> * TELEPHONE: 410-706-7442
TITLE> *
VCLOSE: Closing unit 90 with status "KEEP"

CHARMM>

CHARMM> read param card name par_all27_na.inp
VOPEN> Attempting to open::par_all27_na.inp::

PARAMETER FILE BEING READ FROM UNIT 90
TITLE> * \\\\ CHARMM27 ALL-HYDROGEN NUCLEIC ACID PARAMETER FILE ////
TITLE> * \\\\\\\\\\\\\\\\\\ DEVELOPMENTAL ////////////////////////
TITLE> * ALEXANDER D. MACKERELL JR. AND NICOLAS FOLOPPE
TITLE> * AUGUST 1999
TITLE> * ALL COMMENTS TO ADM JR. EMAIL: ALEX,MMIRIS.AB.UMD.EDU
TITLE> * TELEPHONE: 410-706-7442
TITLE> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
VCLOSE: Closing unit 90 with status "KEEP"

CHARMM> set seg 1
Parameter: SEG <- "1"

CHARMM> ! Read Sequence
CHARMM> OPEN READ UNIT 13 CARD NAME "ADE.pdb"
VOPEN> Attempting to open::ADE.pdb::
OPNLGU> Unit 13 opened for READONLY access to ADE.pdb

CHARMM> READ SEQUENCE PDB UNIT 13
MAINIO> Sequence information being read from unit 13.
TITLE> *

RESIDUE SEQUENCE -- 1 RESIDUES
ADE

CHARMM> ! generate segment mysp30 and set up internal coordinate table
CHARMM> GENERATE RNA1 SETUP
NO PATCHING WILL BE DONE ON THE FIRST RESIDUE
NO PATCHING WILL BE DONE ON THE LAST RESIDUE
GENPSF> Segment 1 has been generated. Its identifier is RNA1.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 1 Number of residues = 1
Number of atoms = 33 Number of groups = 5
Number of bonds = 35 Number of angles = 60
Number of dihedrals = 88 Number of impropers = 2
Number of HB acceptors = 9 Number of HB donors = 3
Number of NB exclusions = 0 Total charge = -1.00000

CHARMM> ! rewind the protein data bank file for reading for reading of coordinates
CHARMM> REWIND UNIT 13
REWINDING UNIT 13

CHARMM> ! read the pdb coordinates
CHARMM> READ COORDINATES PDB UNIT 13
SPATIAL COORDINATES BEING READ FROM UNIT 13
TITLE> *

** WARNING ** For atom in coordinate file, could not find residue in PSF, and is thus ignored:

SEGID= RESID=167 RESNAME= ADE TYPE= P
*** LEVEL 1 WARNING *** BOMLEV IS 0

** WARNING ** For atom in coordinate file, could not find residue in PSF, and is thus ignored:

SEGID= RESID=167 RESNAME= ADE TYPE= O1P
*** LEVEL 1 WARNING *** BOMLEV IS 0

** WARNING ** For atom in coordinate file, could not find residue in PSF, and is thus ignored:

SEGID= RESID=167 RESNAME= ADE TYPE= O2P
*** LEVEL 1 WARNING *** BOMLEV IS 0

** WARNING ** For atom in coordinate file, could not find residue in PSF, and is thus ignored:

SEGID= RESID=167 RESNAME= ADE TYPE= O5'
*** LEVEL 1 WARNING *** BOMLEV IS 0
** WARNING ** After reading, there are no coordinates for selected atom: 1 1 ADE P
** WARNING ** After reading, there are no coordinates for selected atom: 2 1 ADE O1P
** WARNING ** After reading, there are no coordinates for selected atom: 3 1 ADE O2P
** WARNING ** After reading, there are no coordinates for selected atom: 4 1 ADE O5'
** WARNING ** After reading, there are no coordinates for selected atom: 5 1 ADE C5'
** WARNING ** After reading, there are no coordinates for selected atom: 6 1 ADE H5'
** WARNING ** After reading, there are no coordinates for selected atom: 7 1 ADE H5''
** WARNING ** After reading, there are no coordinates for selected atom: 8 1 ADE C4'
** WARNING ** After reading, there are no coordinates for selected atom: 9 1 ADE H4'
** WARNING ** After reading, there are no coordinates for selected atom: 10 1 ADE O4'

** A total of 33 selected atoms have no coordinates

** MESSAGE ** 22 atoms in coordinate file were outside the specified sequence range.
*** LEVEL 2 WARNING *** BOMLEV IS 0

CHARMM> CLOSE UNIT 13
VCLOSE: Closing unit 13 with status "KEEP"

CHARMM> ! print coordinates to output file missing coordinates
CHARMM> ! (hydrogens) are asigned values of 9999.0
CHARMM> PRINT COORDINATES

COORDINATE FILE MODULE
TITLE> * NONE *
TITLE> *
33
1 1 ADE P 9999.000009999.000009999.00000 RNA1 167 0.00000
2 1 ADE O1P 9999.000009999.000009999.00000 RNA1 167 0.00000
3 1 ADE O2P 9999.000009999.000009999.00000 RNA1 167 0.00000
4 1 ADE O5' 9999.000009999.000009999.00000 RNA1 167 0.00000
5 1 ADE C5' 9999.000009999.000009999.00000 RNA1 167 0.00000
6 1 ADE H5' 9999.000009999.000009999.00000 RNA1 167 0.00000
7 1 ADE H5''9999.000009999.000009999.00000 RNA1 167 0.00000
8 1 ADE C4' 9999.000009999.000009999.00000 RNA1 167 0.00000
9 1 ADE H4' 9999.000009999.000009999.00000 RNA1 167 0.00000
10 1 ADE O4' 9999.000009999.000009999.00000 RNA1 167 0.00000
11 1 ADE C1' 9999.000009999.000009999.00000 RNA1 167 0.00000
12 1 ADE H1' 9999.000009999.000009999.00000 RNA1 167 0.00000
13 1 ADE N9 9999.000009999.000009999.00000 RNA1 167 0.00000
14 1 ADE C5 9999.000009999.000009999.00000 RNA1 167 0.00000
15 1 ADE N7 9999.000009999.000009999.00000 RNA1 167 0.00000
16 1 ADE C8 9999.000009999.000009999.00000 RNA1 167 0.00000
17 1 ADE H8 9999.000009999.000009999.00000 RNA1 167 0.00000
18 1 ADE N1 9999.000009999.000009999.00000 RNA1 167 0.00000
19 1 ADE C2 9999.000009999.000009999.00000 RNA1 167 0.00000
20 1 ADE H2 9999.000009999.000009999.00000 RNA1 167 0.00000
21 1 ADE N3 9999.000009999.000009999.00000 RNA1 167 0.00000
22 1 ADE C4 9999.000009999.000009999.00000 RNA1 167 0.00000
23 1 ADE C6 9999.000009999.000009999.00000 RNA1 167 0.00000
24 1 ADE N6 9999.000009999.000009999.00000 RNA1 167 0.00000
25 1 ADE H61 9999.000009999.000009999.00000 RNA1 167 0.00000
26 1 ADE H62 9999.000009999.000009999.00000 RNA1 167 0.00000
27 1 ADE C2' 9999.000009999.000009999.00000 RNA1 167 0.00000
28 1 ADE H2''9999.000009999.000009999.00000 RNA1 167 0.00000
29 1 ADE O2' 9999.000009999.000009999.00000 RNA1 167 0.00000
30 1 ADE H2' 9999.000009999.000009999.00000 RNA1 167 0.00000
31 1 ADE C3' 9999.000009999.000009999.00000 RNA1 167 0.00000
32 1 ADE H3' 9999.000009999.000009999.00000 RNA1 167 0.00000
33 1 ADE O3' 9999.000009999.000009999.00000 RNA1 167 0.00000

CHARMM> ! construct hydrogen positions
CHARMM> HBUILD
PRNHBD: CUToff Hydrogen Bond distance = 0.5000 Angle = 90.0000
CuT switching ON HB dist. = 3.5000 OFf HB dist. = 4.0000
CuT switching ON Hb Angle = 50.0000 OFf Hb Angle = 70.0000
ACCEptor antecedents included
All hydrogen bonds for each hydrogen will be found
Hydrogen bonds between excluded atoms will be kept


NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec FSHIft VATOm VFSWIt
BYGRoup NOEXtnd NOEWald
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 0 atom pairs and 0 atom exclusions.
There are 0 group pairs and 0 group exclusions.
with mode 5 found 95 exclusions and 75 interactions(1-4)
found 9 group exclusions.

CUToff Hydrogen Bond distance = 0.5000 Angle = 90.0000
CuT switching ON HB dist. = 3.5000 OFf HB dist. = 4.0000
CuT switching ON Hb Angle = 50.0000 OFf Hb Angle = 70.0000
ACCEptor antecedents included
dihedral PHI STePs for spin = 10.0000
cutoff for water acceptor search CUTWat= 7.5000

WARNING FROM HBUILD:
Attempt to construct a hydrogen bonded to the atom RNA1 167 ADE C5' with unknown coordinates.
*** LEVEL 0 WARNING *** BOMLEV IS 0
BOMLEV HAS BEEN SATISFIED. TERMINATING.



/---------
/
/
/
! XXXX XXXX !
! XXXX XXXX !
! XXX XXX !
! X !
-- XXX /--
! ! XXX ! !
! ! ! !
! I I I I I !
! I I I I !
/
-- --
---/
XXX XXX
XXXX XXXX
XXXXX XXXXX
XXX XXX
XXX XXX
XXXXX
XXX XXX
XXX XXX
XXX XXX
XXXXX XXXXX
XXXX XXXX
XXX XXX


Execution terminated due to the detection of a fatal error.

ABNORMAL TERMINATION
MAXIMUM STACK SPACE USED IS 72000
STACK CURRENTLY IN USE IS 940
MOST SEVERE WARNING WAS AT LEVEL 0
HEAP PRINTOUT- HEAP SIZE 10240000
SPACE CURRENTLY IN USE IS 4202
MAXIMUM SPACE USED IS 5696
FREE LIST
PRINHP> ADDRESS: 1 LENGTH: 10235798 NEXT: 0

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 2.31 SECONDS
CPU TIME: 1.83 SECONDS
"

Re: problem in generating RNA
temuchin #1548 06/01/04 09:46 PM
Joined: Sep 2003
Posts: 250
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Joined: Sep 2003
Posts: 250
One error is probably due to that you start counting the atoms from 3576 and forth. Try e.g. the "offset" command, or renumber the atoms (starting from one) . You might also encounter problem with the format of the pdb-file..

Re: problem in generating RNA
temuchin #1549 06/01/04 09:56 PM
Joined: Sep 2003
Posts: 8,479
rmv Online Content
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The PSF your script creates has ADE as residue 1, while the PDB file has ADE as residue 167; you need to fix that. A couple ways:

[1] edit the PDB file
[2] use the OFFSET feature of READ COOR, e.g.:

READ COORDINATES PDB UNIT 13 OFFSET -166

Also, ADE isn't a complete molecule; you need some patches in your GENErate statement to deal with that as well, e.g.

GENERATE RNA1 SETUP FIRST 5PHO LAST 3TER


Rick Venable
computational chemist

Re: problem in generating RNA
rmv #1550 06/02/04 09:05 AM
Joined: Nov 2003
Posts: 68
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Posts: 68
Hi there and thanks for your replies.
i used the offset keyword and it seemed to work fine,
but when i used "GENERATE RNA1 SETUP FIRST 5PHO LAST 3TER"
i had an abnormal termination, due to the impossibility of finding an atom called ADE O5T.
anyway, when i used "GENERATE RNA1 SETUP FIRST 5TER LAST 3TER"
it worked ok.
thanks ,
t.

Last edited by temuchin; 06/02/04 09:13 AM.
Re: problem in generating RNA
temuchin #1551 06/02/04 08:05 PM
Joined: Sep 2003
Posts: 8,479
rmv Online Content
Forum Member
Online Content
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Joined: Sep 2003
Posts: 8,479
There are no coords for ADE O5T in your PDB file. You can assign coords to the atom via IC BUILD. If you want the 5' phosphate, try the following, after reading the PDB coords but before HBUILD:

ic purge ! CLEANUP IC TABLE
ic param ! GET MISSING BOND AND ANGLE DATA FROM PARAMS
ic fill preserve ! UPDATE VALUES FROM KNOWN CARTESIAN COORDS
ic build ! PLACE ANY ATOMS WITH UNKNOWN COORDS

Basically, you must place all heavy atoms before using HBUILD.


Rick Venable
computational chemist


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