summary: adding hydrogen using charmm

Hello, everyone:
     The day before yesterday, I post a problem about adding hydrogen to
 a pdb file using charmm. And in the past two days, I received many reply
 about my problem, and now I solve the problem.
     In fact, my problem is not the problem of adding hydrogen, but
 reading coordinate. I put a segid name of 'prot' in the last column of
 pdb file, and the problem was solved. Here I put all the reply in this
 email, and thank all of you who reply me.
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 From: ablondel (+ at +) pasteur.fr
   You have a problem reading the coordinate (no N,CA,C,O for amino
 acid 1...). There must be a name mismatch between psf and pdb. Change
 the pdb accordingly, if appropriate. It seems reasonable that you
 cannot build the Hs on a missing N. An advise "learn" to read the
 output of charmm carefully. The problem is most of the time signalled
 but it may be hundreds of lines before the crash. As a rule of thumb
 read every line of output and correct the input until you don't have
 any more warnings that may cause a problem.
 From:  alex (+ at +) outerbanks.umaryland.edu
 the charmm pdb reader is not great.  one suggestion is
 to write the coordinates (write coor pdb unit xx) after
 doing the generation.  all the coordinates will be 9999.
 but it will allow you to see the format that charmm is
 looking for.
 also, do
 ic fill
 ic para
 ic build
 before
 hbuild
 From: surjit (+ at +) lctn.u-nancy.fr
 Charmm needs a pdb file that has a segname as the last column. So you
 need to modify the input pdb file a little for Charmm to appreciate
 that. For eg here is a  line from a normal pdb file and the
 corresponding one that Charmm appreciates.
 Normal pdb
 ATOM      1  O1  BTN     1       0.311  -4.640  15.789  1.00  0.00
 Charmm PDB
 ATOM      1  O1  BTN     1       0.311  -4.640  15.789  1.00  0.00
 BTN
 The last column is the segname is call in the psf file.
 From: lozg (+ at +) mail.rochester.edu
 It seems that your input file for charmm is ok, but the PDB file is not
 ok. Generally I will encounter this problem when I just download a
 structure from PDB and throw it to CHARMM. I don't know exactly what
 is going on, but it is quite possible that the format of the PDB is
 not acceptable by CHARMM. So, what I do is, write a Fortran program to
 change the downloaded PDB file to a card file, and serve the CHARMM with
 the card file.
 From: rvenable (+ at +) gandalf.cber.nih.gov
 Actually, you seem to be having a problem with reading coords from the
 PDB file.  Also, your IC commands aren't quite right (you don't want IC
 FILL), and should probably precede the HBUILD-- you *must* make sure all
 heavy atoms have coords before calling HBUILD.  Here's the way I read in
 a PDB file for a peptide:
 open unit 3 read card name meltna.pdb
 read sequ pdb unit 3
 rewind unit 3
 gener a setup warn first glyp last ct2
 ! SETUP UNIVERSAL COORD I/O FOR PDB; BETTER THAN read coor pdb
 read univ
 pdb
 w  61  6
 end
 read coor univ unit 3 sele .not. type H* end
 close unit 3
 ic param ! FILL IN MISSING VALUES FROM PARAM FILE
 ic purge ! CLEANUP IC TABLE
 ic build ! BUILD COORDS FROM IC
 ! FORCE REBUILD OF ALL H ATOM COORDS
 coor init sele type H* end
 hbuild sele type H* end
   From: syn (+ at +) ibms.sinica.edu.tw>
 ! read in NMR coordinates
 OPEN READ UNIT 11 CARD NAME -
 /home/user/marios/rnase/crd/1rch_15.crd
 READ COOR CARD UNIT 11 FREE
 CLOSE UNIT 11
 ! build missing coordinates
 IC FILL PRESERVE
 IC PARAMETERS
 IC BUILD
 ! place the hydrogens
 HBUILD
 It is better to use CHARMM use their own coordinate file.
      From: torsten.becker (+ at +) iwr.uni-heidelberg.de
 your problem is not  building the hydrogens, but reading the
 coordinates.
 Charmm does not read in the coordinates of your system:
 >  ** 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
 >
 charmm does read the coordinates from your pdb, but cannot find a
 corresponding
 atom in the system you did setup. Charmm identifies a system via a
 segment ID
 (segid). Since charmm stells you 'segid=   ', i guess you forgot to
 specify
 the segid in your pdb file. You gave your first segment the name 'prot'
 . This
 name must be specified in your pdb file, when reading coordinates from
 it. I
 don't know the exact format now, but in each ATOM/HETATOM line after the
 B-factor entry you have to put prot.
 From: ed (+ at +) bioorganic.ucsb.edu>
 Hello, you need to rewind unit 1 before you can
 read the coordinates. When you use the " read sequ pdb"
 command it reads to the end of the file. When the second
 command "read coor pdb" comes the file is still at the
 end so it finds no coordinates. The following should work
 ! 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
 rewind unit 1
 ! rewinding the coordinate file
 open unit 1 card read name 1pef.pdb
 read coor pdb unit 1
 close unit 1
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   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 |  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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