AMBER: "Atom valence violated" from LEaP

From: Francesco Pietra <>
Date: Mon, 5 Nov 2007 03:00:28 -0800 (PST)

I am using DOCK6.1 and Amber9 with a pore protein model.

>From the model deprived of the single (natural) residue HOH from the pore, I
could carry out the whole sequence grid scoring and amber rescoring. The only
way I found to get the whole sequence passing, was by removing all hydrogen
atoms from the model, placing TER records to get rid of long (50A) bonds, and
let LEaP build the prmtop and inpcrd files, which could be taken from Chimera
1.2422, 17 Oct07 build for DockPrep, etc.

Now I wanted to repeat all the above sequence with the natural residue HOH in
place, separated by a TER record. Here is the last portion of the pdb file now
used for LEaP:

ATOM 3412 O THR X 444 -15.798 15.199 24.830 0.00 0.00 O

TER 3413 THR X 444

HETATM 3414 O HOH X 448 -0.036 0.094 -2.262 0.00 0.00 O


Now, LEaP did the job, though grid generation in Chimera complained (on loading
the mol2 file generated from these prmtop and inpcrd files) that

WARNING: assign_vdw_labels: Atom valence violated for xxxx.inpcrd
*** WAT445 445 H1 6886
Error in reading receptor

Chimera was right. The internal water residue was now triangulated. The H-H
bond error was not in creating the mol2 file with DocPrep: loading the prmtop
and inpcrd files from LEaP to either Chimera or VMD shows that the water
molecule is triangulated, three bonds, O-H, O-H, and H-H. The error was in LEaP
(or, obviously and most likely, in the operator).

The last portion of the coordinate section of the mol2 reads:

 6884 OXT -13.9375 14.3278 24.9443 O.co2 444 THR444 -0.8044

 6885 O -0.0360 0.0940 -2.2620 O.t3p 445 WAT445 -0.8340

 6886 H1 0.9212 0.0940 -2.2620 H.t3p 445 WAT445 0.4170

 6887 H2 -0.2760 1.0206 -2.2620 H.t3p 445 WAT445 0.4170

and that mol2 ends with:

   443 GLU443 6857 RESIDUE 4 A GLU 2

   444 THR444 6872 RESIDUE 4 A THR 1

   445 WAT445 6886 RESIDUE 4 A WAT 0 ROOT

Must add that the model before removing all hydrogen atoms showed the HOH
residue correctly, i.e. two bonds.

Perhaps the protocol to follow is different from the one I followed. Removing
all protein hydrogens and leaving res HOH intact? How? Or any better idea.


francesco pietra

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Received on Wed Nov 07 2007 - 06:07:21 PST
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