[phenixbb] LigandFit (distorted manesium hexahydrate cluster)

Hasan Demirci demircha99 at gmail.com
Tue Dec 28 12:07:36 PST 2010


Dear All,
I am trying to run " LigandFit " with the following hydrated magnesium
hexahydrate cluster (without the hydrogens) pdb.
"HETATM    7  MG  MG6 A   1     -53.936 117.342  91.273  1.00128.70      A   MG
HETATM    2  O1  MG6 A   1     -55.351 117.224  89.749  1.00128.62      A    O
HETATM    3  O2  MG6 A   1     -52.532 117.421  92.718  1.00127.25      A    O
HETATM    4  O3  MG6 A   1     -55.370 118.284  92.428  1.00127.74      A    O
HETATM    5  O4  MG6 A   1     -53.253 119.219  90.518  1.00128.43      A    O
HETATM    6  O5  MG6 A   1     -54.385 115.379  91.937  1.00127.84      A    O
HETATM    7  O6  MG6 A   1     -52.566 116.391  89.994  1.00128.62
 A    O  "

LigandFit automatically runs the elbow and creates a new search pdb
file with hydroges and while doing this, elbow totally screws up the
original starting geometry of the Oxygen atoms within the cluster
after the addition of hydrogens.
"HETATM    1  MG  MG6 A   1     -53.913 117.323  91.231  1.00128.70
  A   MG
HETATM    2  O1  MG6 A   1     -55.140 117.947  90.141  1.00128.62      A    O
HETATM    3  O2  MG6 A   1     -53.080 118.061  92.589  1.00127.25      A    O
HETATM    4  O3  MG6 A   1     -55.453 117.480  92.061  1.00127.74      A    O
HETATM    5  O4  MG6 A   1     -52.768 118.528  90.669  1.00128.43      A    O
HETATM    6  O5  MG6 A   1     -53.676 115.727  91.923  1.00127.84      A    O
HETATM    7  O6  MG6 A   1     -53.363 116.194  90.004  1.00128.62      A    O
HETATM    8  H11 MG6 A   1     -55.461 117.161  89.473  1.00128.62      A    H
HETATM    9  H21 MG6 A   1     -52.333 117.378  92.967  1.00127.25      A    H
HETATM   10  H31 MG6 A   1     -55.430 118.350  92.700  1.00127.74      A    H
HETATM   11  H41 MG6 A   1     -53.300 119.422  90.378  1.00128.43      A    H
HETATM   12  H51 MG6 A   1     -54.636 115.255  92.077  1.00127.84      A    H
HETATM   13  H61 MG6 A   1     -52.319 116.372  89.793  1.00128.62
 A    H  "

Is it a bug or am I making something wrong?
Does the search pdb HAVE TO be covalently linked? or can I search for a cluster?

Thanks.


-- 
Hasan DeMirci



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