Subject: [modeller_usage] modelling with water again
From: jo hanna <>
Date: Wed, 4 Jan 2006 00:33:28 +0000
Hello
Many thanks for the advice Walid, I have done as you have suggested and
have made some progress but still am not seeing the behaviour that I am
expecting.
I have been using the pap format for the alignment as this has being
working better and have tried the following varied options in the top
and align files, I should also mention that in my pdb i have the exact
number of ligands(2), and single water that i would want to include in
my model
Option 1:
remove water_io command from top file,
try X for water and not w therefore at end of alignment
structure = /..W
and seqeunce = /...
this gives this error:
rdabrk__290E> Number of residues in the alignment and pdb
files are different:
517 516
For alignment entry: 1
recover____E> ERROR_STATUS >=
STOP_ON_ERROR:
1 1
Option 2:
water_io = on in top file, in alignment file, structure end aligmment = /..X seqeunce end alignment = /...
gives this error
rdabrk__291E> Sequence difference between alignment and pdb :
Option 3:
water_io = on in top file, end of alignments, strcuture = /..w seqeunce = /...
This combination creates a model but there is no mention in the logfile
of the BLK residues or of whether the water is accepted and in the
final model the water O is written as a BLK residue. From previoud
posts i was expecting a message in the log file re the TIP3 water and
also for the model to contain a HOH or OH2 and not a BLK.
Option 4:
water_io = on in top file and end os alignments strcuture = /..w seqeunce = /..w
This once agaian produces the out of range error
delete__443_> Restraints marked for deletion were removed.
Total number of restraints before, now:
51247 47550
nselat__596E> Atom index is out of range (iatm,natm): 4033 4032
recover____E> ERROR_STATUS >=
STOP_ON_ERROR:
1 1