Hi,
 
Water is indicate by "w" in an alignment file and any one of HOH H2O OH2 MOH or WAT in a PDB file (cf modlib/restyp.lib). TIP3 is not a valid PDB file residue code, it is a 4 character CHARMM code (not the PDB code) for the water residue. PDB files use only 3 characters for residue codes, a CHARMM atom file may use up to 4 characters.
 
The warning about the OH2 atom in the TIP3 residue was written out because the TIP3 PDB residue code is unknown to MODELLER. Still, probably the resulting model will not change much when you use the PDB water residue code instead of TIP3.
 
All the best, Andrej

--
Andrej Sali, Associate Professor
The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540
e-mail sali@rockefeller.edu; http://salilab.org

-----Original Message-----
From: lsettimo@ra.abo.fi [mailto:lsettimo@ra.abo.fi] On Behalf Of Luca Settimo
Sent: Monday, January 21, 2002 4:18 AM
To: sali@rockefeller.edu
Subject: reask

Sorry if I reask, but for me it´s very important information.
Thanks in advance if you can help me...
 

Hello, I have one problem when I try to model water molecules.
I check your FAQ and previous email... but I canno´t solve.
I indicated water molecules 'w' in the alignment file,

I edited my template (I replace HETATM with ATOM) like that in the end
(using the right numeration of course also in the alignment):
 

ATOM   1975  O   BLK   263      78.930  33.505  36.595  1.00 20.17
or
ATOM   1975  O   TIP3   263      78.930  33.505  36.595  1.00 20.17
or
ATOM   1975  O   OH2   263      78.930  33.505  36.595  1.00 20.17

... but in any case when I run modeller happens this:
 
 

>> CHECK_ALIGNMENT:
 

chkseq__E> sequence difference between alignment and pdb :
   STRUCTURE RES_IND  ALN_ITYP  ALN_RES  X_ITYP  X_RES  -----*-----
           1     260        28     TIP3      82   BLK   KGECEw----

chkaln___> Checking structure-sequence alignments:
           Implied target CA(i)-CA(i+1) distances longer than  8.0
angstroms:

ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
----------------------------------------------
    258     1  261   262      C     E   25.243
 

<< end of CHECK_ALIGNMENT.
 
 

iatmcls_W> MODEL atom not classified: TIP3:OH2
 

patchss__> Number of disulfides patched in MODEL:      1
patchss__> Disulfide created between:   203  CYS   203      258  CYS
258
iatmcls_W> MODEL atom not classified: TIP3:OH2
 
 
 

In the end the model is created with the water (so it seems that everything work except this message) but why it writes like that?
What I have to do to model the water (do I have to treat like BLK or like TIP3?)
 
 

...................................................................

Luca Settimo
Molecular Structures and Biocomputing
Department of Biochemistry and Pharmacy
Åbo Akademi University Tykistökatu 6A 20520 Turku Finland
phone: +358 (0) 2 2154600
fax: +358 (0) 2 2153280
mobile phone: +358 50 5238418
mailto:lsettimo@abo.fi
http://www.abo.fi/~lsettimo