AMBER: Puzzle with WAT

From: Francesco Pietra <>
Date: Sat, 17 Nov 2007 10:14:38 -0800 (PST)

I am faced by a recurring puzzle with WAT (standard TIP3).

In Amber9 xleap I loaded a pore protein_noH.pdb model getting top and crd files
In both Chimera and VMD these showed that the WAT oxygen atom (natural, inside
the pore) had been added of two hydrogens with intramolecular bonding between
the two hydrogens. Otherwise, the geometry was correct for water.

Correspondingly. in Chimera dockprep complained that one hydrogen of that WAT
had incorrect valency, and refused to proceed.

The protein.pdb created with ambpdb from such top and crd files showed the WAT
correctly, without intramolecular H-H bonding. The geometry was exactly the
same as for the above "wrong" WAT. With this protein.pdb, Chimera's dockprep
was happy. That allowed docking with various (big) ligands, including amber
re-score. I posted to dock-fans that the issue was solved, and how.

Now I wanted to carry out Amber9 MD of that protein-ligand complex, inserting
it into a lipid bilayer. I first tried the above protein.pdb alone into a
membrane. A new venture for me.

I posted separately a question how to create a hole around the protein.
However, even when that is solved, I am faced again by the problem of viewing
WAT into the pore as a triangle. Also, the many WAT mixed to the POPC of the
membrane are also viewed as triangles. Actually, when that protein.pdb is
loaded to xleap (as before leaprc.ff99SB and leaprc.gaff), the WAT into the
pore is seen as a triangle.

Thus, the protein.pdb, created with amdpdb is good for viewers and dockprep and
docking, not back for LEaP. Although, it may seem as a loop, these are the
facts (that so far I am unable to understand).

I did not try yet if that allows MD, just because going on with such
triangulated water seems unsafe.

The protein.pdb ends as follows:

ATOM 6885 O WAT 445 -0.036 0.094 -2.262
ATOM 6886 H1 WAT 445 0.921 0.094 -2.262
ATOM 6887 H2 WAT 445 -0.276 1.021 -2.262

The membrane.pdb ends as follows:

ATOM 50316 O WAT 3357 47.120 46.103 -26.069 1.00 0.00 W45 O
ATOM 50317 H1 WAT 3357 46.727 45.819 -26.895 1.00 0.00 W45 H
ATOM 50318 H2 WAT 3357 47.214 47.052 -26.153 1.00 0.00 W45 H

as a representative of the many WAT present.

francesco pietra
(the membrane was created with VMD and the file rearranged to be understood by Amber9)

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Received on Sun Nov 18 2007 - 06:08:04 PST
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