--
Andrej Sali, Associate Professor
The Rockefeller
University, 1230 York Avenue, New York, NY 10021-6399
tel +1 212 327 7550;
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e-mail ; http://salilab.org
-----Original Message-----Sorry if I reask, but for me it´s very important information.
From: [mailto:] On Behalf Of Luca Settimo
Sent: Monday, January 21, 2002 4:18 AM
To:
Subject: reask
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:
http://www.abo.fi/~lsettimo