problem of add hydrogens using CHARMM
- From: Mao Xiang <xmao : at : iris.sipp.ac.cn>
- Organization: iris.sipp.ac.cn
- Subject: problem of add hydrogens using CHARMM
- 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 |
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