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 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?)

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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