Subject: problem of add hydrogens using CHARMM

From: Mao Xiang <[email-masked]>
Date: Mon, 20 Nov 2000 11:55:18 +0800

Hello:
    I am a newman in CHARMM program, I met a problem when used it to add
hydrogen to a protein molecule. The input file is the following:

-------------------------------------
* Generate PSF and CHARMM coordinate set for 
* the small protein Echistatin
*

! Read in Topology and  Parameter files

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

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

! Read sequence from the PDB coordinate file
open unit 1 card read name 1pef.pdb 
read sequ pdb unit 1 

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

generate prot setu

! read in pdb coordinate file 

open unit 1 card read name 1pef.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 1pef.psf 
write psf card unit 27 
* PSF for echestatin 
*

open unit 1 card write name 1pef-allh.pdb 
write coor pdb unit 1
* echestatin  Structure with hydrogens
*
close unit 1

stop 
--------------------------------------------------------
And a part of the output file is the following:

=----------------------------------------------
      
 CHARMM>    ! Read sequence from the PDB coordinate file
 CHARMM>    open unit 1 card read name 1pef.pdb
 VOPEN> Attempting to open::1pef.pdb::
 OPNLGU> Unit  1 opened for READONLY access to 1pef.pdb
  
 CHARMM>    read sequ pdb unit 1
 MAINIO> Sequence information being read from unit   1.
 TITLE>  *

          RESIDUE SEQUENCE --    18 RESIDUES
          GLU GLN LEU LEU LYS ALA LEU GLU PHE LEU LEU LYS GLU LEU LEU
GLU LYS LEU 
 ***** Message from SEQRDR ***** THE SYSTEM CONTAINS  7 TITRATABLE
GROUPS
 THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE
AND RTF
 HIS -  0  ASP -  0  GLU -  4  LYS -  3  TYR -  0
  
 CHARMM>     
  
 CHARMM>    ! now generate the PSF and also the IC table (SETU keyword)
 CHARMM>     
  
 CHARMM>    generate prot setu
 THE PATCH 'NTER  ' WILL BE USED FOR THE FIRST RESIDUE
 THE PATCH 'CTER  ' WILL BE USED FOR THE LAST  RESIDUE
 GENPSF> Segment   1 has been generated. Its identifier is PROT.
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues  
=       18
         Number of atoms         =      328   Number of groups    
=      100
         Number of bonds         =      328   Number of angles    
=      609
         Number of dihedrals     =      882   Number of impropers 
=       43
         Number of HB acceptors  =       28   Number of HB donors 
=       31
         Number of NB exclusions =        0   Total charge =   -1.00000
  
 CHARMM>     
  
 CHARMM>    ! read in pdb coordinate file
 CHARMM>    open unit 1 card read name 1pef.pdb
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit    1 with status "KEEP"
 VOPEN> Attempting to open::1pef.pdb::
 OPNLGU> Unit  1 opened for READONLY access to 1pef.pdb
  
 CHARMM>    read coor pdb unit 1
          SPATIAL COORDINATES BEING READ FROM UNIT  1
 TITLE>  *

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

  SEGID=     RESID=1    RESNAME= GLU  TYPE= N   
 *** LEVEL  1 WARNING *** BOMLEV IS    0

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

  SEGID=     RESID=1    RESNAME= GLU  TYPE= CA  
 *** LEVEL  1 WARNING *** BOMLEV IS    0

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

  SEGID=     RESID=1    RESNAME= GLU  TYPE= C   
 *** LEVEL  1 WARNING *** BOMLEV IS    0

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

  SEGID=     RESID=1    RESNAME= GLU  TYPE= O   
 *** LEVEL  1 WARNING *** BOMLEV IS    0
 ** WARNING ** After reading, there are no coordinates for selected
atom:     1     1 GLU  N   
 ** WARNING ** After reading, there are no coordinates for selected
atom:     2     1 GLU  HT1 
 ** WARNING ** After reading, there are no coordinates for selected
atom:     3     1 GLU  HT2 
 ** WARNING ** After reading, there are no coordinates for selected
atom:     4     1 GLU  HT3 
 ** WARNING ** After reading, there are no coordinates for selected
atom:     5     1 GLU  CA  
 ** WARNING ** After reading, there are no coordinates for selected
atom:     6     1 GLU  HA  
 ** WARNING ** After reading, there are no coordinates for selected
atom:     7     1 GLU  CB  
 ** WARNING ** After reading, there are no coordinates for selected
atom:     8     1 GLU  HB1 
 ** WARNING ** After reading, there are no coordinates for selected
atom:     9     1 GLU  HB2 
 ** WARNING ** After reading, there are no coordinates for selected
atom:    10     1 GLU  CG  

 ** A total of   328 selected atoms have no coordinates

 ** MESSAGE **   153 atoms in coordinate file were outside the specified
sequence range.
 *** LEVEL  2 WARNING *** BOMLEV IS    0
  
 CHARMM>    close unit 1
 VCLOSE: Closing unit    1 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    ! build in hydrogens if using a crystal structure
 CHARMM>    hbuild sele all end
 SELRPN>    328 atoms have been selected out of    328
 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  SHIFt    VATOm    VSWItch 
     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.
 <MAKINB> with mode   5 found    937 exclusions and    879
interactions(1-4)
 <MAKGRP> found    291 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 PROT 1    GLU  N   
with unknown coordinates.
 *** LEVEL  0 WARNING *** BOMLEV IS    0
 BOMLEV HAS BEEN SATISFIED. TERMINATING.
=====================================================================================================

I wish you can help me solve this problem. Thanks.

Regards,
mao xiang

  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|  Xiang Mao                                                     |
|  Lab of Molecular Regulation for Microbial Secondary Metabolism |
|  Shanghai institute of Plant Physiology, Academia Sinica        |
|  300 Fenglin Road, Shanghai, China, 200032                      |
|  Tel: +86-21-64042090-4791                                      |
|  Fax: +86-21-64042385                                           |
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~